Not all that much gay imo, but the chemistry between them (and every actor in every combination imo) is pretty awesome. With Will and Hannibal, it's to the point where people watching the show were still shocked when Hannibal, obviously harms Will only with extra obviousness about it.

Also, Hannibal's actor doesn't just eye fuck, he eye salivates, and ends up looking like he's about to jump everyone.