Staying anywhere near Javitz is going to be expensive.
I agree the hotel shuttle ferry is the easiest logistically assuming it is running. Beyond that I see two options:
1) bus to Port Authority (42nd & 8th) and walk or take the M42 bus to Javitz. (If you do this, you need to buy metrocards and watch the sign on the bus. The M42 has two stopping points.) Personally, I'd walk.
2) bus from Weehawken to Hoboken and PATH to Penn Station (33rd & 6th.) The walk is probably about the same. Two long avenues (6th to 8th) vs 8 short blocks. It's a more fun walk though as you get to walk past Macys and through a touristy area. From 42nd and 8th, you get to wak through a bus depot area. You can also take the M34 bus from 6th to Javitz but it is a pokey bus so again, I'd walk. PATH is $1.75 and you can buy cards for it as well.
If I was going, I'd take the ferry or go with option 2. Mainly because option 2 is the most fun. If you're visiting NYC, you should see more than just Javitz
.
Have a good trip to New York City!