I live on a small lake in southern NH that has alewife in it. Today my buddy and I went out and were catching smallmouth in the middle of no where on topwater, jerkbaits and swimbaits because they were chasing the bait. What we noticed is that 90% of the time, the bait was not busting on the surface. Where we were catching them was at random. We were fishing over 30-40 feet off of a grass drop off where the wind was blowing. After we fished out the spot, we had no where else to go, because we did not know where we could find the bait. What are places that we should target to find suspended bait.

That's a tough one man.  There are no real rhymes or reasons aside from water temperature as to where they'll be it seems.  Even water temperature isn't always a predictor.  Up on Champlain on the same day I've seen them in 4-6' weedy bays and near the surface in 40' as well as down in the thermocline (50') in 80'.