(at around 5 mins) Robert Hays played a pilot in the beginning and said he has "been through worse" flying through a storm. This was a reference to him flying in Airplane! (1980) and Airplane II: The Sequel (1982).
The pilot played by Robert Hays is named "Bob Wilson". William Shatner's character in The Twilight Zone (1959) episode Nightmare at 20,000 Feet (1963), where he thought he saw a monster on the wing (much like Ian Ziering did here with the shark), was named "Bob Wilson".
Opening scenes: The plane cutting through the clouds like a shark through water, and the pilots discussing whether they had the fish or chicken for dinner are a direct nod to Airplane! (1980), with the aforementioned Robert Hays, once again, playing a pilot.
The characters played by Mark McGrath and Kari Wuhrer are named Martin and Ellen Brody. Those are the same names as Roy Scheider and Lorraine Gary's characters in Jaws (1975). Their son is named Vaughan, which was the name of Murray Hamilton's character as the Mayor in Jaws (1975).
(at around 36 mins) The sewer workers make two "Star Wars" references back-to-back. "Something just moved past my leg" is a quote from Luke Skywalker in the trash compactor scene of Star Wars: Episode IV - A New Hope (1977). They are also trying to shut off valve #1138, a number that appears frequently throughout the Star Wars saga.
Anthony C. Ferrante: (at around 35 mins) the film's director appears as the guitar playing crooner in the subway.