How much time at the Intrepid depends on your interest level. I'm interested in aviation and served on an aircraft carrier, so spent the entire morning looking at airplanes, exploring the ship, examining exhibits, and touring the submarine, etc. I could have spent more but I had to meet the family, who had no interest in joining me to see airplanes. I noticed other visitors who arrived at about the same time I did found 1-2 hours sufficient.
Can't speak to the parking as we were spending a long weekend in Manhattan and I just walked to the ship from my hotel. However, when I sailed on the Magic a month ago, we were docked within easy walking distance (I think it was two piers over).