It's perfectly fine to use face-to-face or telephone metaphors when referring to online interactions. We haven't coined new terms for all the modern modes of interaction on the Internet. Much computer-related terminology is based on metaphors from the physical world, e.g. "desktops".
I think most people would say "talk to you tomorrow", since it accurately describes what they're doing in a voice-only call. But in informal conversation, when the context makes the mode of interaction clear, and it's not necessarily visual, you can use other words like "see you" (as Cascabel said in a comment, it's common for blind people to use the phrase "see you" even though they're incapable of doing it literally).
If you need to be specific, you can say things like "skype you tomorrow" -- some dictionaries have added this as a generic verb, e.g. Lexico
Have a spoken conversation with (someone) over the Internet using the software application Skype, typically also viewing by webcam.
‘my parents want to know when is a good time to Skype me’
I've also heard people use "Facetime" as a verb.