By Robin Respaut and Dave Graham

SAN JUAN, Puerto Rico, Sept 28 (Reuters) - Thousands of people lined up at San Juan harbor on Thursday to board a cruise ship that will take them from Puerto Rico to the U.S. mainland in one of the largest evacuations since Hurricane Maria slammed Puerto Rico more than a week ago.

Maria, which came ashore as the strongest storm to hit the island in nearly 90 years, has created a humanitarian crisis. The powerful storm knocked out the nation's electric grid and has crippled communications networks, transport and the water supply for the territory's 3.4 million people.

The devastation is likely to feed an exodus that has driven tens of thousands of Puerto Ricans from the economically struggling island in recent years in search of opportunity on the mainland.

"I'm sorry to be leaving Puerto Rico, but I have to. I prefer home, but it's impossible with these conditions," said Ada Reyes, 85. She was in a wheelchair and traveling on the Royal Caribbean cruise ship bound for Florida with her granddaughter, Maria Fernanda, 19.

Fernanda planned to drop her grandmother in Florida, then head to Boston to look into colleges. A second-year student at the University of Puerto Rico, the teenager did not know when classes there would resume.

Royal Caribbean International said its Adventure of the Seas cruise ship will carry 3,800 passengers from Puerto Rico and the U.S. Virgin Islands. A company spokesman said the cruise line is providing the passages free of charge and that travelers were registered with the help of local officials.

The ship will make humanitarian calls in the hurricane-hit U.S. Virgin Islands, where it will drop off supplies. It will then head to Fort Lauderdale, Florida, with a planned arrival of October 3.

The cruise line said it will work with airlines to make travel arrangements for passengers looking to meet up with friends and family on the mainland.

"This is a humanitarian mission on behalf of Royal Caribbean," company spokesman Owen Torres said.

At San Juan's main airport, flights are slowly returning. Major carriers including Southwest and JetBlue are still operating at reduced schedules as the airport works to restore power and return to full staffing levels.

JetBlue typically has about 40 flights a day to Puerto Rico but on Thursday it had only seven, which it said was still more than any other airline flying to the U.S. territory.

ONE WAY OR ROUND TRIP?

People have waited for days for a flight out, with some Puerto Ricans wondering if they will stay once they reach the U.S. mainland.