Back during all of the post-September-11th cuts, WDW did suspend the POR-to-Downtown Disney boat service, but they restored it last spring. (I rode it in March of this year.) I am fairly sure that they are still running it.
I think the boat service is wonderful, especially if the weather is nice. It is more relaxing than dealing with the bus service, and is enjoyable enough that I would use it at least once per POR stay even if I didn't have any particular need to visit Downtown Disney!
The times that it runs may vary seasonably, but last time I was there it started about 4:00 PM and ran until about midnight.
The boat service is just one of many good reasons to stay at POR...Enjoy your stay!
Talk about a magical moment, we got to see the space shuttle liftoff from the DTD boat to POR last week. The captain stopped the boat so we could all look and attempt to take pictures.