I don't think there's a 'correct' size as such, as I believe the banner area on the Bootstrap theme that you're using will expand to accommodate whatever logo height you are using.

However, I agree that it does look a bit odd, but perhaps this is as much to do with the white border around the logo as it is the size of the logo?

I think I would aim to crop out as much of the border as possible, and then make the rest transparent (save as a PNG file since JPEG doesn't support transparency), or the same colour as the background.

You could also try the Fresh theme as this uses a white background on the banner area and so the logo border won't be visible. Or experiment with the other banner options available with the Bootstrap theme.

To try things out you may want to use the test site version of your site, though do read the notes on the test site first!

Thanks

Joe