I had the same problem and doing these steps worked: use AppCleaner to uninstall Evernote empty my trash bin restart my Mac re-download app. from evernote.com and re-install. I'm not sure if 1 and 2 were necessary but using AppCleaner definitely was as uninstalling by just dumping the app. in the trash bin did not fix things. Thanks blahblahunknown for opening this and DTLow for the suggestion.
Sorry to resurrect an old thread but it was left incomplete and it appears in Google results. LocalSystem mentioned being able to do what the OP was asking for but didn't give an explanation. Now, in the Mac App at least, right-clicking inside a table and selecting "Tables->Table Properties" gives options for changing the line color and background. It is also accessible if the cursor is within a table and you go through the toolbar at the top of the screen "Format->Tables->Table Properties."