Since you're asking on the game development forum, I'm assuming you're interested in a game development career. Both programs would be fine. They have some overlap, but they also would lead you in different directions.
A traditional computer science program is aimed at the more theoretical aspects of computing. You'd generally work in more traditional languages (C/C++/Java) and you'd spend a lot of time contemplating data structures, algorithms, and efficiency. CS majors typically are required to take a great deal of Math and Science. (I encourage our students to get a Math minor, because they're only one course away by the time they take our requirements.) The focus on math and theory are good preparation for certain kinds of game programming (say building game engines and creating lighting models.)
Software engineering has a different focus. Software engineering programs are typically more focused on business applications. The emphasis is on working with large teams of developers and building large software projects. Games are a form of business application, so the skills would be applicable.
Plenty of CS majors move into software engineering as they gain experience, but fewer people seem to move into CS after they've studied software engineering.