1.) Would going to Boppard or Rüdesheim give me a longer boat ride, as I'd like to make the most of it. (Having a hard time finding distances online.)
Cruising to Boppard makes the cruise longer - from Bingen, Boppard is 2.3 hours, whereas St. Goar is 1.5 hours.
STARTING the cruise in R'heim instead of Bingen adds 15 minutes more to your boat time. But these are completely useless minutes since all you are doing is crossing the river over to Bingen. You see nothing more. Map of the area:
http://www.loreley-info.com/eng/rhein-rhine/walking-hiking.php
2.) Boppard and Goar were both mentioned at end points . Which would provide the longest and most beautiful ride, and perhaps an opportunity to hop off and on? Or are there other end points you recommend?
Hopping off the boat more than once gets tricky and time consuming. There are only 5 KD boats per day going north and they don't always arrive when you're ready to leave.
The most beautiful segment to cruise is between Bingen and St. Goar. Going further to Boppard is alright, but not as spectacular (and depending on weather conditions and your mood, the longer boat ride can actually get a little tedious.) I like Boppard but I did not recoommend Boppard as an end point mostly because of your limited time and because St. Goar has the biggest sightseeing pull - Rheinfels Castle. Better to stop there and skip Boppard, I think. And IMHO Bacharach is the town with the most beautiful buildings if you want to do a stopover. So my rec. remains Bingen > (Bacharach) > St.. Goar in your situation.
3.) Do you know if there are less touristy, smaller boats that go down the Rhine?
Both Bingen-Rüdesheimer and KD are tourist sightseeing boats full of tourists. The only boats the locals use are the ferries at the ferry crossings (see map.)
4.Are there particular companies you recommend?
The one whose boat is departing at a time that is convenient for your schedule that day.
If you were staying the night and sightseeing over 2 days, my rec's would be completely different. Boppard has a great chairlift ride. Braubach has an amazing medieval castle, more interesting than Rheinfels Castle ruins, IMHO. There's more in this area to see and do that you are omitting on a 1-day outing from Cologne.