I took a closer look at the traction tires on the Long Island RS-3 this morning and as I turned the wheels I realized the reason they looked lumpy was that the traction tires were not put on properly--the lumps were actually just spots where the traction tire was too close to the flange and was riding up, causing what looked like a bump. I straightened out the traction tires and it helped, but the wobble didn't go away, it just wasn't as bad.
I noticed that the locomotive wobbled less while it pulled several cars than it did when running light (not pulling any cars). I also noticed (and this is counter-intuitive) that when I ran the locomotive at postwar speeds (you know, fast, faster, fastest) there was actually a lot less wobble than when it was running at low speeds, so if I buy the Long Island passenger cars that go with this loco I'll be running it pretty fast when it's not pulling into or out of a station.
If I find that the wobble still bugs me, I'll try to the foam rubber trick that Ed mentioned.