What do you and your sister enjoy doing together? Maybe plan a girls day centered around what she enjoys- a day of shopping, a trip to a museum, maybe check into a nice hotel or BnB for a night and order room service and watch cheesy movies...
Maybe also get her a gift that's personal- if she does charms, maybe a Pandora new mom charm, or a piece of jewelry with the baby's birth stone it, or something like that???
I'm sure she'll understand why you might not be able to make it to her shower, but you could a nice gift ahead of time or maybe make her a little "shower in a box" with baby items and some treats for herself.