Can you swap out just the cranks for shorter ones? Or does the whole crankset including the chainrings have to be replaced? I have a Bontrager triple.

You could swap out the arms and reuse the chainrings if:

1) the chainrings are compatible with the new arms (bolt pattern, mounting configuration)
2) the arms are compatible with the current bottom bracket. For example, you can only use ISIS splined bottom brackets with ISIS crank arms.

As an example, this page shows a bunch of available crankarms, some with chainrings, some without.

https://www.jensonusa.com/store/sub/1...ts.aspx?s=1257