Old Town Trolley Tours of San Diego
DESCRIPTION: Enjoy a circular 32-mile tour of San Diego and Coronado in tour-friendly wheeled trolleys that have been running since 1989. Tour guides are knowledgeable about the history and anecdotes of the region - they don't mind tossing in a few jokes either.  If your timing is right when crossing the Coronado Bridge, you'll see NAVY Seals jumping from helicopters into the bay for training exercises. You can hop on or off at any stop along the way, but be sure to watch the time, since time flies when you're having fun. If you only plan to ride the trolley from end-to-end, it takes 2 hours so be sure you've eaten in advance and carry bottled water with you. Considering that you can leave you car parked all day while hopping on-off to see about 75% of the main tourist attractions, the tour is a great value. Best places to board downtown are Harbor Drive at Broadway and at Seaport Village. The tour includes a free souvenir map of the route.
CREDIT CARDS: yes
WEBSITE: http://www.trolleytours.com/san-diego

SEAL Tours
DESCRIPTION: If you a mild sailor's perspective of San Diego Bay, this is your tour. Operated by the same company as Old Town Trolley Tours, affable narrators know their craft as you enter a modified tour bus, that once it enters the water, changes its form of locomotion to that of a motorboat. The narrator is full of entertaining chatter about every nuance of the bay from the laziest sea lion to the sharpest fishing pelican. No need to worry about the narrator getting distracted about your safety in the vessel. A certified captain guides the ship while the other person  narrates. The tour last about 90 minutes. Best places to board downtown are Harbor Drive at Broadway and at Seaport Village.
CREDIT CARDS: yes
WEBSITE: http://www.sealtours.com

San Diego Harbor Excursions
DESCRIPTION: One and Two hour San Diego Bay tours depart every 75 minutes. In the summer cruises hours run longer. One Hour Tour South cruises by USS Midway Museum, Coronado Bridge, Naval Amphibious Base and Destroyers, NASSCO Shipbuilding Facility and the Hotel Del Coronado. One Hour Tour North cruises by North Island Naval Air Station, Naval Submarine Base, Star of India, Cabrillo National Monument, Sea Lions and Dolphin Training Center, and Fort Rosecrans Cemetery. Two Hour simply combines both tours. Coronado Ferry also plies the San Diego Bay to North Island and Coronado. By tickets and board at Harbor Drive near Broadway. Check prices at their shared website.
ADDRESS: 1050 North Harbor Drive
PHONE: 619-234-4111
WEBSITE: http://www.SDHE.com

Mission Bay Cruises
DESCRIPTION: For those who prefer another taste of historical boating while near Sea World, the Bahia Belle stern wheeler has evening cruises. For info about bay cruises charter boats, and diving in San Diego
WEBSITE: http://www.sdwaterfront.com

San Diego Cruise Port
DESCRIPTION: Featuring a spectacular natural harbor in the southwestern tip of the United States, San Diego is becoming a major Port of Call for the West Coast cruise industry whose routes span from Seattle to the Mexican Riviera, and are increasing in frequency. Royal Caribbean, Carnival, Celebrity, Norwiegian, Holland America and smaller cruise lines now have claim a San Diego port of call. You may drive onto the pier by presenting your ID and a ship ticket for sailing on that specific date. All luggage must have your name and address attached. You will be required to show a passport and cruise ticket to enter the cruise terminal.
ADDRESS: Harbor Drive at Broadway
PHONE: 619-686-6200 port office
WEBSITE: http://www.sandiegocruiseport.com/cruise-san-diego-cruise-ships.html

Royal Caribbean International
Offers 4, 5, 7, 9, 10, 11 and 12-night cruises to the Mexican Riviera; 11 and 13-night cruises to Alaska; 13, 14 and 15-night cruises to the Mexican Riviera, Panama Canal and the Caribbean
WEBSITE: http://www.royalcaribbean.com

Carnival Cruise Line
Offers 3, 4, and 5-day cruises to Baja Mexico; 8 and 9-day cruises sail to the Mexican Riviera
WEBSITE: http://www.carnivalcruise.com

Holland America
Offers 15 and 16-day Circle Hawaii cruises for 7, 8, 10 and 14-days in the Sea of Cortez/Mexican Riviera cruises 3, 4 and 11-day Canada cruises, 15, 18, 19, 26 and 28-day Panama Canal cruises; 35-day South America cruises and more
WEBSITE: http://www.hollandamerica.com

Celebrity Cruises
Offers a 14-night Alaska cruise and 13, 14, and 17-night Panama Canal cruises
WEBSITE: http://www.celebritycruises.com