2.Bxe6+ throws away a piece for no reason, so it's a confusing variation you give.
As for your question. 2.Qxd4 Nxc2+ is definitely better for white than throwing away a piece.
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To find the best defense (or at least, the best one you're able to find, none of us are computers) calculate each line, render an evaluation in your mind for the end position (not necessarily a number, but who you think is better and why) then, finally, compare the two evaluations. That's basically what analysis is.
Other than counting material in most positions I usually put an emphasis on minor pieces. Whose are better. Of course there are other things like king safety, who controls an open file, etc, but almost always it's worth it to imagine the end position in your mind, and carefully look at the minor pieces too.
So here's what I did
OK, I had this position OTB, black (me) to move. Not sure when I started seeing these kind of moves, but my eyes were immediately drawn to 1. ..Qxd4!, which I played without really looking at all continuations (I did, of course, see the knight fork following 2. Qxd4).
My opponent responded with 2. Bxe6+ , and the game continued Bxe6 3. O-O-O Nxa2+ 4. Nxa2 Qxd2+ 5. Qxd2 Bxa2 6. b3, trapping the a2 bishop, but ultimately giving me a net 3 pawns once that bishop was traded for the b3 pawn.
Looking at it, it's hard to say if 2. Qxd4 Nxc2+ followed by 3. Nxd4 is better or worse than this, I was fairly well convinced that 2. Nxe6 was worse due to Qxe5+. Whenever I play a combo like this, I want to know (1) whether it is sound, and (2) what the best defense against it would have been.