Reddington didn't set Tom up. Either he set himself up to take the fall (along with Zanetakos,) for the Fokin murder, or
Tom set up Reddington.
Above I suggested that Reddington could have controlled events by hiring Zanetakos for the bombing. On this hypothesis, the order for the bomb was placed when Reddington learned of the box. Then when Tom confronted Elizabeth, Reddington speeded up the time table to 36 hours. This explains why Reddington let Elizabeth "overhear" a conversation (one-side, if there were even two,) otherwise essential to the resolution. This explains how Reddington could have contrived to give Zanetakos Tom's picture. This even explains yet another remarkable coincidence, Zanetakos losing her phone (but not killing Ressler.)
Of course Reddington wanting to save his Lizzie from hearbreak, even at the expense of making himself look bad, makes a pretty far-fetched "martyr for love" fantasy.
On the other hand, Tom setting Reddington up would be a much easier and more straight-forward plot except for one huge problem. Namely, how could Tom have been sure that Zanetakos would be captured alive, to confess? Without her confession, he'd still be a suspect. I suppose it's possible that I'm wrong for assuming the writers actually have a coherent plot, but it seems too early to take away benefit of doubt.
PS Could the "Tom is framing Reddington" scenario be saved if Ressler is Reddington's man? Also, was the symbol on Zanetakos' getaway stash the same as on the one in the Keen household? Also, does a week's time passing in each episode (as Ressler's line about seven weeks suggests) feel right?