“Cowboy beans” are usually the same as charro beans (frijoles charros; frijoles a la charra).  Sometimes “cowboys beans” is another name for simply “pork and beans.” (See the 1993 and 2007 citations below.) Usually, however, the dish starts with pork and beans and adds hamburger (not always an ingredient in “charro beans”).
   
The name “cowboy beans” is cited in print from at least 1928.
   
 
Wikipedia: Cowboy beans
Cowboy beans is a bean dish popular in the United States. The dish consists of beans and ground beef in a sweet and tangy sauce. The flavor is similar to baked beans but with a southwestern twist. Although cowboy appears in the name, the use of canned beans, ketchup, and BBQ sauce means the dish is unlike anything ranch hands would have eaten. Cowboy Beans are served stewed or baked, depending on the recipe. A typical recipe might include:
 
Pork and Beans
Chili beans (canned pintos in a flavored sauce)
Ground Beef
Onion
Pepper
Ketchup
BBQ Sauce
Brown Sugar
 
It’s unclear how Cowboy beans got their name or where they originated from. They are easy to prepare and variations on the recipe are available on the internet and in cookbooks and cooking magazines.
 
Cooks.com
COWBOY BEANS  
1 lb. hamburger
1 med. onion
1 can pork ‘n beans
1 can chili
1/2 c. water
 
Brown hamburger and onion. Add pork ‘n beans, chili and water. Simmer until water is cooked down. Serve with corn bread.
 
18 March 1928, San Antonio (TX) Express, pg. 3, col. 2:
Barbecued young goat, calf and pork was available in generous quantities, along with the inevitable cowboy beans and everything else that goes with it.
 
4 April 1940, Paris (TX) News, pg. 9 ad:
COWBOY BEANS
No. 300 Size
Mexican Style
4 for 27c
(Piggly Wiggly supermarket—ed.)
 
29 January 1950, Denton (TX) Record-Chronicle, “Cornpone, Cowboy Beans By Shands,” cook book supplement, pg. 5, col. 2:
Ranch Style Beans
1 Cup pinto beans, soaked in cold water for 1 or 2 hours until nearly tender. Then add:
1 Large onion chopped
1 Small can tomatoes
1 Teaspoon salt
2 Tablespoons bacon droppings
Continue to simmer slowly until all ingredients are well done and the flavor blended thoroughly.
 
6 July 1958, Long Beach (CA) Independent Press-Telegram, “Chef of the Week: Montie Montana Is Cowboy Beans Fan” by Mildred K. Flanary, pg. W8, cols. 1-2: 
COWBOY BEANS
2 cups navy beans
1 clove garlic
1 large onion, cut coarsely
1/2 pound fat salt pork, ham or bacon
1 dried red chili
1 teaspoon salt
 
Soak beans overnight in plenty of cold water. Place meat in large kettle and brown slightly. Add beans and cover with cold water. After boiling starts, add other ingredients and simmer, with lid pressed tightly, until done. Serves 4.
 
25 August 1967, El Paso (TX) Herald-Post, pg. A9, col. 2:
COWBOY BEANS is the title of the winning recipe sent in by Mrs. A. R. Marston of 321 Coral Hills drive. Cook 3 cups of dried pinto beans in 4 cups of water for about three hours or until fairly tender. Add a generous tablespoon of salt (more if taste calls for it); 1 teaspoon of black pepper, one small onion, chopped, 2 tablespoons of red chili powder, 1/4 cup of bacon drippings and simmer another hour. In a frying pan, cook 1 pound of ground beef until it loses its red color and separates into particles. Add meat and drippings to beans along with a small can of tomatoes. Allow to simmer several hours longer and
 
14 March 1971, Mansfield (OH) News Journal, pg. H8, col. 4:
COWBOY BEANS
Brown in skillet
1/2 pound ground beef
1 small onion
1/2 green pepper
6 strips of bacon
Pour off grease and add a cup of water and 1 stalk of chopped celery. Simmer 15 minutes.
Mix in casserole
1 large can baked beans
1 large can kidney beans
1 large can baby lima beans
1/2 cup brown sugar
1 tablespoon worcestershire sauce
salt and pepper to taste
Mix with skillet mixture and bake in oven.
Mrs. Ed Haudenschild
Rd 2, Loudonville, O
 
15 May 1973, Oneonta (NY) Star, pg. 35A, col. 3:
COWBOY BEANS
Mrs. Charles Sheldon
RD2 Otego, N. Y.
Ingredients
2 tbsp. butter
1 pound hamburger
1 envelope onion soup mix
2 1 pound cans pork and beans
1 1 pound can kidney beans
1 cup catsup
2 tbsp. prepared mustard
2 teas. cider vinegar
Method: Brown meat in butter. Stir in remaining ingredients. Pour into 2 1/2 quart casserole or bean pot. Bake at 400 degrees for 30-40 minutes. Makes 8-10 servings.
Kids love it.
 
Google Books 
It Works for Us!
Proven Child-Care Tips for Experienced Parents Across the Country
by Thomas L. McMahon
New York, NY: Pocket Books
1993
Pg. 43:
...pork and beans is called “cowboy beans”;...Carol A. Nelson, Memphis.
 
Google Books
The Book of Regional American Cooking
by Janeth Johnson Nix
Los Angeles, CA: HP Books
1993
Pg. 77 (Southwest):
COWBOY BEANS
1 pound dried pinto beans, sorted, rinsed and drained
8 cups water
1 (1-1/2-lb.) ham shank
2 medium-size onions, chopped
2 garlic cloves, minced
1 teaspoon ground cumin
1 teaspoon dried leaf oregano
1/2 teaspoon salt
2 limes
 
Place beans in a large kettle. Add enough water to cover beans by 2 inches. Cover and let stand overnight. or cover and bring to a boil. Boil 2 minutes. Turn off heat and let stand, covered, 1 hour.
 
Drain beans, and add the 8 cups water. Add ham shank, onions and garlic. Boil 10 minutes. Reduce heat. Simmer, with lid ajar, 2 hours. Remove shank; cut meat into bite-size pieces.
 
Return meat to pan and add cumin, oregano and pepper. Continue to simmer until beans are very tender, about 1 more hour. At end of cooking, beans should have a little liquid. If beans become dry, add more water. If beans are too soupy, continue to cook, stirring occasionally, until desired consistency. Add salt to taste starting with 1 teaspoon. Cut limes into wedges; pass at the table to squeeze over each serving.
 
Makes 6 to 8 servings.
 
New York (NY) Times
February 1, 2006
Quick Cowboy Beans
Adapted from “Mexican Everyday,” by Rick Bayless (W.W. Norton, 2005)
Time: 30 Minutes

4 thick slices bacon, cut into small pieces
2 garlic cloves, peeled and finely chopped or crushed through a garlic press
1 15-ounce can diced tomatoes in juice (preferably fire-roasted)
2 15-ounce cans pinto beans (do not drain)
1 or 2 canned pickled jalapeños, more to taste
Salt
½ cup chopped cilantro.
 
1. In a large (4-quart) saucepan, cook bacon over medium heat until crisp, about 4 minutes. Add garlic and stir for a minute, then add half the tomatoes with their juice (reserve other half for another use). Cook, stirring, for 3 to 4 minutes. Add beans with their liquid and simmer over medium-low heat for about 15 minutes.
2. While beans simmer, stem chilies, cut in half lengthwise and scrape out seeds. Chop into small pieces and add to beans.
3. Taste beans and season with salt if necessary. Ladle into small bowls, sprinkle with cilantro and serve.
Yield: 4 to 6 servings.
 
Google Books
Remembering Mrs. O’Donald:
Growing, Learning and Teaching
by Mary Mayesky Holroyd
New York, NY: Vantage Press, Inc.
2007
Pg. 10:
The one I remember the most was “cowboy beans.” That was her name for plain old pork and beans. She knew that I wanted to grow up to be a cowgirl and move out west. So, she dubbed these humble beans “cowboy beans.” With a title like that I was at least willing to try them. And I found out I liked them.