Your parking fees will end up being more than your minivan rental if you drive into Manhattan every day. On top of the usual $40+ daily fees, generally there is a surcharge for oversize vehicles such as a minivan.
If you are staying in Flushing near the subway, hopefully it is near the Number 7 ("The Flushing Line"). That will take you directly into midtown with stops both at Grand Central Station and Time Square.
It sounds like you are coming in this weekend which means you should have great weather. So you might want to start with a little cruise around the southern half of Manhattan:
http://www.circleline42.com/site/scheduling_pricing.aspx?Product=2
http://photography.robertondrovic.com/Landscapes/The-Big-Apple/6633570_hC9DK#423023308_3eBHM
The 2 hour cruise is good since going around the northern part of the city doesn't add much of a view other than Yankee Stadium and the George Washington Bridge so you can save the time and money by skipping the 3 hour full island tour.
Since you have your wife and parents with you, consider the sunday matinee performance of Mamma Mia on Broadway (this also gives you the chance to walk around Times Square.
http://www.mamma-mia.com/broadway/broadway.asp
Save the long lines for the Empire State Building and go to the Top of the Rock by buying a "timed ticket" in advance:
http://www.topoftherocknyc.com/
Then pick a clear night to go to the top of the Empire State Building (less of a line at night and spectacular views:
Take walk through Central Park including Belvedere Castle (where the weather station is located) and the Bow Bridge:
If you like art, check out the Metropolitan Museum of Art and the Museum of Modern Art:
Met
MOMA
Also, explore the Bronx by seeing the Orchid Show at the Botanical Gardens:
http://www.nybg.org/
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And if there is any interest in seeing a famed cathedral or two, start with St. Patrick's in midtown but also consider St. John the Divine.
Finally, if you are going to eat in Chinatown and are bringing your parents you might want to pick a little nicer place than where the "locals" eat (and I am including myself in that from college days - - - anyone remember late nights at Wo Hop's?) and go for the peking duck at The Peking Duck House on Mott Street. Make sure you get an order of the steamed dumplings as well.
http://www.pekingduckhousenyc.com/