The ending of Ice Age: Continental Drift settles three separate stories, and in my opinion it handles the family one best.
First, the villain. Manny beats Captain Gutt in a final fight, and Gutt is eaten by a siren, so the sea he ruled as a pirate captain finishes him off. Granny's sea monster, Precious, has already helped drive off the pirates, which gives the sea voyage an odd, comic payoff: the creatures of the deep end up on the herd's side. It is also the kind of set piece the filmmakers planned carefully. According to Animation World Network, the team previsualized the big storm sequence and ran a seasick test with 3-D glasses to check how the wave motion felt, so the ocean climax was built to be felt rather than only watched.
Second, the family. Peaches has realized her new friends are shallow and has made up with Louis, and with Ellie and the others rescued, the household is whole again. It could be argued that this is the real resolution, because the film started with a father who could not let his daughter grow up and ends with her having chosen her own friends well. It also pays off a thread from Ice Age: Dawn of the Dinosaurs, where Manny was anxious about becoming a father at all. Ice Age: The Meltdown had him worrying that he was the last mammoth alive, so this saga has now taken him from loneliness to fatherhood to letting a teenager go. Ice Age: Collision Course continues that line, with Peaches engaged to Julian.
Third, the herd. They settle on a lush island where the hyraxes can rebuild their home, and Shira joins them as Diego's partner. That pays off the bond that formed while she was supposed to be his captor, and it gives Diego something the earlier films never did, a relationship of his own.
Then comes Scrat. Chasing a map shaped like an acorn, he reaches the lost city of Scratlantis, which sinks and leaves him stranded in a desert. In my opinion it is a fitting last gag, since the film began with his acorn chase splitting the continents and finishes with him losing yet another prize. The same engine drives the saga's other openers: his acorn also sets the asteroids in motion in Collision Course. For where the saga goes next, the Ice Age movies in order page shows the full sequence.