If it's on JBA HQ 4, that's how the level ends. You disarm the bomb where Emile was originally standing and then the SWAT team breaks in only to find that you've disappeared. If you got the 'best' ending you'll then be taken to NY Harbor for the 'boat' mission with Moss.
[EDIT]There is one problem in that if you have used distractions to move the guards away from the bomb in HQ 4 and they return just as you get it disarmed, they will kill you as the swat team comes in. This can sometimes be avoided by dropping some smoke grenades (available in the upstairs armory before going down the elevator) just before you do the third part of the disarm procedure.[END EDIT]
If it's the NY Harbor mission, you MUST get off the boat before they blow it up. There are only two ways to make it out:
1. After disarming the bomb quickly crouch and run out the door to your left. The game will take over and you'll jump off just as the boat is destroyed.
2. After disarming it, crouch and head for the ladder to the left of the door (inside the cabin). Climb down and exit the side door, hop over the rail and drop into the water and quickly swim away.
I personally like the second method, even though it's more difficult, because you actually control Sam's escape rather than the cutscene escape.
NOTE:
Depending on which method you choose, you need to watch your onscreen radar to pick the time to disarm when the guards are furthest away from your desired exit point so they won't shoot you to death before making your getaway!