I only know Erie from the Buffalo end. The NFTA smallboat harbor is an exellant launch and you'll be on prime spots within minutes of rounding the outer breakwall. One good place to start is in front of the windmills, you'll know what I am talking about when you get there. Idle around in 30-35 fow till you see a change in the bottom (humps,shoals, rockpiles, ditchs, etc) some may be only a few yards in size, some may be 1000's. Toss out a marker where you first notice the change, and then again, when it drops back off. Then drift over this spot with either a tube jig, or a dropshot rig. If this spot produces drift it several times, if not find another, there are millions of them. If it's calm and you are marking fish on your graph on any of these spots, it's a blast to lower a dropshot rig down to each fish and watch the arch come up and bite it. I have a buddy who is great at this, and I have done it some.
If it's rough on the lake, forget the river, if you were coming in the spring I would say just fish in side the break walls, as they often hold good fish, but I have no idea in the fall. But like I said forget the river, it's not that great for SM, some OK LM in spots, but I don't know it well. My first choice if it's too rough to fish Erie is to drive either the hour SW on the thruway to Chautauqua Lake, or an hour east too Conesus Lake, one of the western most finger lakes, and IMHO the best bass lake of the fingers.