Can this knight move level the game? As clearly black cannot trap the white queen for longer. So, won't Nxd4 be the best move in this scenario? Letting the queen escape and take a piece for his lost rook. Nxd4 will be followed by either Nxc2 or Nxe6. What are the different ways in which white can counter this move?

Q1bq3r/p1ppk1bp/1pn1B1pn/4PpN1/3P4/8/PPP2PPP/RNB1K2R b KQ - 0 1

1... Nxd4
This is a funny looking position, which I assume you probably reached out of a poorly played Dutch defense, something along the lines 1.d4 f5 2.Nf3 g6 3.Ng5 Bg7 4.e4 e6 5.Bc4 Nh6 6.Qf3 b6 7.Bxe6 Ke7 8.e5 and so on... (or 1.d4 f5 2.Nf3 g6 3.Ng5 Bg7 4.e4 e6 5.Bc4 Nh6 6.Qf3 b6 7.e5 Ke7 8.Qxa8 Nc6 9.Bxe6) which are very weird looking...

With little analysis I think you convince yourself that black is completely lost here and Nxd4 doesn't come to rescue either. Simply put, white is a clear piece up, the queen isn't really trapped, black's king is a mess, and there's just not any piece coordination to create any counter-play whatsoever. As pointed out by TMM in the comments after Nxd4 white just retreats the bishop to b3 and protects everything, this is the simplest and best move. Or even Bc4 to preserve the bishop and even provoke Nxc2+ which leads to some fun tactics either mating the black king or trapping the queen, for example:

Q1bq3r/p1ppk1bp/1pn1B1pn/4PpN1/3P4/8/PPP2PPP/RNB1K2R b KQ - 0 1

1... Nxd4 2.Bc4 Nxc2+ 3.Kd1 Nxa1 4.Nxh7 Ke8 (4...Nf7 5.Bxf7 Kxf7 6.Qd5+ Ke8 7.Bg5 ) 5.Bg5