Were the neighbors home at the time?
Honestly, sounds like the beginning of a Trayvon Martin case. Think of how much more flack or possible charges Zimmerman may have gotten had he been under the influence that day. In Nebraska at least if you brandish a firearm it better be because you or someone around you is in imminent danger of bodily harm or death. As I understand if you shoot someone running out of your house with your tv you will be on trial. Lets say someone breaks into your house in the middle of the night, you find them with there arms in the air surrendering with no weapon, they turn to run away and you shoot them you will likely be on trial. When I took my CCW class the instructor said, "if your sleeping at night and you wake up to someone breaking into your house, you are suppose to grab your gun, huddle in the corner, call the police, and wait there(unless you have a child in another room that may be in danger).
To me seeing a couple of guys checking doors so you brandish a firearm, especially while intoxicated, sounds like a very bad idea. Granted they were likely up to no good as they did run away when you confronted them, but you can't assume they were up to no good just because they walk around a house and check some doors. Example: I have a friend who, when we make plans to go shooting or hang out, says to just come over at whatever time and walk in the house. At times he forgets to leave the door unlocked. If a neighbor saw me "checking doors" which I do when the usual door is locked, and decided to come over and point a gun at me and tell me not to move, if I was fast enough he/she likely would find themselves looking down a barrel as well. Either outcome to follow is not a good outcome.
Then you add in the I can hold them until the police come. There are a lot of different scenarios that could result. They could run away or just leave (at which point you can't use lethal force), or they could come at you and you would be forced to use lethal force. The police have to prove that they were doing something wrong. So if all they do is walk around the house and you say they check a couple doors, they really haven't done anything that bad...yet. So if you are able to hold them there until the police arrive, you have now used the threat of lethal force to force a couple of guys who walked around your neighbors house and checked some doors. I could see charges of kidnapping or false imprisonment on your part, unless they could link them to some other crime that had occurred and depending on what officers show up and what kind of mood they are in.
To try to "hold" someone until the police arrive is a bad idea. If the perp(s) weren't really stupid, they would know they could/would just walk/run away. You couldn't stop them and you could not shoot them. When I was younger I was held at gunpoint by a farmer who I had unknowingly trespassed on his property. When the cops arrived they warned him not to be brandishing a firearm in an unwarranted situation, and simply told me to leave and not come back.
IMO, if you are under the influence and see this happening, A. call the police and stay in your house B. call the neighbors, warn them, and still stay in your house
If you were not under the influence I think you have 2 options, both start with calling the police.
A. Call the police and stay in your house, if you do this it may be possible (still unlikely though) that the police may arrive in time to see/catch the perps, where as if you run them off they are not going to catch them.
B. Arm yourself (concealed), and politely ask them, "what are you guys doing here" "what business do you have here" or something along those lines. Then if they do have a reason to be there they can explain this to you and you/they can make sure everything is ok. If they are up to no good they will likely run away which is what happened in your case. Or if they have really bad intentions they may draw a weapon or come at you in which case you would be justified to use deadly force.
Bottom line though: Alcohol+Firearm+confrontation+brandishing = very bad outcome a lot of the time