It appears that (for the time being) Seaport Pizza is operating on a seasonal basis. I have found the location open in the summer months (and spring break) when the park is at it's busiest, but not over recent winter/holiday periods (when the park is also busy). On my most recent trip, it appeared that Seaport Pizza was testing out a "mobile order system", but I never saw a single customer go in, or out of the building over a 10 minute period.
If you really want a slice a pizza, the near-by Expedition Cafe might be able to help you out. Most of their "Italian" menu is various varieties of pizza.
There are some quiet, covered seating areas on the right-hand side of the main pizza pickup windows.
(*) Price ranges listed are the average cost for one main entree and one soft beverage item, unless otherwise stated. There are many combinations of appetizers, deserts and drinks that will add to your final total. Many parks also use seasonal pricing systems which result in food and beverage costs increasing at peak times. Please check with the location that you are interested in for specific pricing information.