FAQ for
Star Trek IV: The Voyage Home (1986) More at IMDbPro »

No - they actually used very detailed animatronics for George and Gracie, and stock footage for a few other scenes. No real whales were used in the movie's production.

The so-called "European Version" features a new prologue that summarizes the events of the previous two movies. The US Version doesn't include these scenes. A detailed comparison between both versions with pictures can be found here.

The crew of the Enterprise travel back in time from 2286 A.D. In 2286, the crew return to Earth about three months after they'd rescued Spock and brought him to Vulcan. However, the majority of the story takes place in the year 1986 A.D., the same year the film itself was released.