The boat from either the Contemporary or MK will be better/faster. They both drop you off right near Pioneer Hall. Otherwise you would still need to take a second internal bus after the first FW bus. Plus, the boat ride is really nice and relaxing.
Also, I would give yourself more than an hour to do the trip. If everything goes right, you might make it in an hour. But, with Disney transportation, things can frequently go less than perfect. I would be safe and plan at least 1.5 to 2 hours. The boat ride from MK is 20 minutes itself.
Lateness can be an actual problem with HDDR. Because it is part show, if you are too late the will not seat you. On the other hand, some nights the entire dining process can be running a bit behind and your timing is less of an issue. That happens more with the last seating of the night.