The only downfall of the boat is that it's more popular, and seats less. It only starts running half an hour before park opening (I think; you can check the sign down at the boat dock)
The bus holds more people, and the stop at another resort takes just a couple minutes. It drops you just beyond where the boat lets you off, at the MK. It also runs a little more frequently than the boat, because it's such a short trip over to the MK. The busses start early enough for EMH. I really don't remember if the MK boat does
Because we're monorail nuts, we took the boat to the CR, then hopped the monorail. The boat to the CR starts running at 7 am, so you can definitely make it for EMH, if you're open to transfers. It takes a bit longer than any other transport options, but if you leave early enough you can make it in plenty of time