A few more:
Cobblestone Road, a few miles west of Voorheesville, is probably the best, and best-known railfan hangout on the Selkirk Branch. The location is just east of the Voorheesville industrial park. The two mains are separated here by a hundred feet or so, and there are good photo angles available in both directions. You can easily park and see stuff coming in time to get out of the car and get into position, and there's enough room to let kids out (with good supervision, as always) and still keep them off the ROW. You'll get scanner0r warning of westbounds as they hit the Voorheesville detector, and if your antenna is good, you'll hear the South Schenectady detector also.
The sun angles are nearly broadside in the afternoon, so it's one of those odd places where you can shoot in both directions for a good portion of the day.
Next, try driving route 5S on the south side of the Mohawk River from Thruway exit 26 west to South Amasterdam. You'll go past the site of Lock 10, which was nearly destroyed during Hurricane Irene last fall, and then actually WAS destroyed by TS Lee a couple weeks later. The park is no longer there, and the lock itself is closed to the public, but there are some good photo angles available from the side of the road. Also, there are still enough slow orders in the area that you can often cruise 5S until you see a train, then donut and catch him somewhere down the line.
5S also goes under the approach to the Mohawk River Bridge, which is in the process of being replaced. The actual construction site is fenced and under video surveillance, but it's a fascinating scene with the bridge half-built, and I've encountered no problems pulling off to the side of the road for a photo. Combined with the "cruise 5S" strategy outlined above, its an excellent place to shoot eastbounds in the afternoon. That's important, since the daily rhythm of traffic seems to put a bunch of eastbounds through after 3 PM or so, when sun angles elsewhere along the Mohawk are terrible. There's a detector at Guy Park, just west of Amsterdam, that gives good warning of eastbounds, but the detector at South Schenectady is (on my scanner anyway) not reliably audible in this area.
In the mornings, try the bridge at French's Hollow, (French's Mill Road, just south of US route 20). It's a knockout photo of the RR on a high bridge, with a dam and waterfall beneath. The downside is that you get no warning whatsoever of approaching trains (either by ear or by the scanner), so you have to stay on station if you want to shoot. The good news is that the highway bridge that you shoot from is blocked off and has no vehicle traffic anymore, so you can sit in a lawn chair, read the paper, and wait until something shows up. Light's good from maybe 2 hrs after sunrise until about 10 AM or so. It's an outstanding place for a take-out breakfast and coffee.