I'll bet if you compare the two, Best Buys offer might not offer the same thing exactly as the T-Mobile deal.
Barring that, Best Buy can more likely than not, get better deals on phones, through volume buying. Best Buy can get models for more than one cell carrier, while the cell carriers and limited to the models that they carry only.
So it's the actual plans and fee connected with those plans (activation and types of plans), where you will see the major difference. Also Best Buy will have a different warranty and return policy than T-mobile has, and may also offer different insurance options. I know that some resellers offer insurance that covers water damage to PDAs, where as T-Mobile's might or might not, just covering, lost/stolen/broken.
I know that depending on where you buy a phone, might make a difference to T-Mobile when you call them for help on phone replacement. If not from them, they may send you back to where you bought it in some cases to get help with replacement.
But all in all, go for the best deal you can find, make sure it's covered at least for the first year with insurance if you tend to be rough/butter fingered with you phones, or tend to leave them behind when out and about.