Riverside is on the D train of the green line, in Newton (closer to Wellesley than to Waltham). you'd have to take it into Kenmore Sq. and then change trains to the E. parking is ample and modestly priced at Riverside.
there is (or at least used to be) a parking lot across a side street from the MFA. not cheap, but convenient. check on mapquest to be sure, but you could take 95 to the mass pike east (I-90), to the Prudential/Copley exit. stay left on the exit ramp, and go toward Prudential (not Copley). this puts you on Huntington, which is the road the MFA is on. it should be a mile or two (?) down Huntington, on the right.
if you don't mind Boston drivers, it's a pretty simple drive (few or no turns). on a Saturday, it's going to be your fastest way by a long shot (as compared to parking at the T--I don't know about the Downeaster).
there are more direct ways there, but this is very simple. (I suspect that if you took 95 to 93 south to Storrow Drive, you could probably get there faster, but you'd have to take more turns.)