We stayed at the Quality Inn & Suites on the River in late June. Nice aspect about it is the river and tracks are right behind the inn. It even has a patio with chairs where you can watch trains and the river go by. It is located just a mile or two west from the center of town off the interstate.
We were out and about during the prime of the day. I'd say I saw a couple of trains in the morning and 2-3 trains in the late afternoon/evening from the inn. We drove through Glenwood Canyon four times over the span of 2 days and never saw a train. I had better luck up on the Craig Branch coming south from Steamboat Springs.