If the previously mentioned save issue isn't the case, I haven't any idea what it could be. Let me get something straight. You were using the alternate travel mod that comes with MR2 and were using the motorcycle to travel back when this happened? To fix, you disabled alternate travel and enabled the default fast travel system. You then fast traveled to Tenpenny and no crash?
I'm using normal save/load from the game menu. I wasn't using motorcycle to travel to the tower (left it at megaton, no fuel ) but going on foot from the tunnels (after killing roy). Anytime I was close to the tower, game crashed. Only solution I came up with was disabling alternate travel (in fomm, didn't knew console command) just to have the ability to fast travel into the tower. Saved after FT in tower, enabled AT back in fomm, loaded and finished the quest without any problems. Since then I've been able to run around the tower with no crashes.