Where is the best place to park for 2hrs for walking on to ride the ferry over and right back?

Yes, use the pay lot.

There is a pay lot at the park across the street.

I believe there is a lot next to the donut shop if I'm correct just make sure you have no valuables in plain sight.

Unless you're driving a Ferrari you can park at the donut shop just don't leave your laptop on the seat. Don't leave it there for very long a 4 or 6 hour trip is fine.