Do I have to killed all of the Legion to get to the bunker or is there anyway to sneak in? Even though I am wearing Legion armour I still get attacked! Help!!!

I sneaked in, stealthboy and crouch. You're probably still going to be attacked by any Legion guards inside the building though. so make sure you have a carbine or similar.

I can sneak in a rifle? I was only able to sneak in a damn knife..( only Melee weapon I had at the time)

no idea. I went to the Fort with Boon, and he killed the gate guards before I even turned around. So I went into camp armed to the teeth (I left Boon by the gate though)

Just don't attack the Legion or enter the Fort with Boon and you should be able to get to the Bunker without sneaking or fighting at all (you'll just need to go visit with Caesar first).

Just pickpocket the Gaurd for the Weapons storage key right by the door and take all your gear back

I was already hated by the legion so only had one option, I turned up there with my best weapons and killed everyone, as a favour to Boone. It was solid & I used about 15 stempacks, I also did alot of running away because of the amount of guards in that place, I was very dissapointed when I got in the bunker I couldnt find any special weapons down there.

I've been through it twice.

If they're taking your weapons, they shouldn't be hostile to you. If they're hostile to you, they never should have taken your weapons.

If you're wearing a disguise, just avoid the guards that can see through it.