If your main reason for attending BC would be the resources of the BTI, I'd choose the GTU. The institutions of the BTI are quite spread apart throughout the Boston area, and, while most places in the area are accessible via public transportation, you may find it a hassle to try and go back and forth. Most of the schools of the GTU, however, are within a few blocks of each other (and, yes, walking from place to place is wonderful on sunny and warm days, which are not at all uncommon in the area).
Also, with regard to non-theological resources, you shouldn't forget that as a student of the GTU, you would have access to the faculty, course offerings, and libraries of UC Berkeley.
One other thing to be said in behalf of the GTU is that, in my opinion, it more radically realizes religious diversity--you can keep your identity, but you'll be forced to do so in constant dialogue with contrasting perspectives. This, of course, is true to an extent of the BTI as well, but, in my experience, diversity is more pronounced at the GTU (perhaps it is simply because the schools are closer together).
That said, for a master's degree, BC would perhaps be a wiser choice for at least two reasons. In the first place, the degree from BC will (I believe) be more valuable when it comes time to apply for PhD programs (but, you didn't say whether the master's your considering re the GTU is the GTU common MA, or, rather, a master's from one of the schools in particular--which could make a huge difference). And, secondly, funding will be more available at BC.
I hope that helps.