Allen has a stronger arm so purely from that perspective, you'd think he'd be more comfortable throwing in the wind than Mac (not to mention he has more experience throwing in this kind of weather than Mac does ... yet).
That said, from a team perspective (coaching, personnel, and philosophy), I tend to think this weather favors the Pats. Bigger OL, better running team, better RBs, perimeter players who are comfortable running with the ball, a strong screen game. The Bills, OTOH, are a pass-first team who uses the pass to setup the run. If they cannot effectively push the ball down-field tonight, that'll be an issue for them.
As the wind currently appears, I don't think any NFL QB, no matter how strong their arm, could consistently, effectively throw in this weather. The only situation that would really worry me would be if the wind calms down a bit, and settles into a spot where it's strong enough to affect Mac's throws but not Allen's; that is the only scenario in which I see the weather advantage really tilting towards Buffalo. Otherwise, I think the inclement weather/wind (generally speaking) is advantage Patriots.