I think that the most important question here is, Does this functionality add functionality to my theme or to my site?
Page templates in general are theme territory and in my opinion should stay in a theme. This does not mean any functionality on which a template depend should be in the theme as well.
These meta boxes that you are talking about can either be theme or site specific, and this is something that you should consider and answer yourself. If you need these to be available even if you switch themes, keep it in a plugin as it will give functionality to your site. If not, keep it in your theme.
Still, there is no wrong doing in keeping this in a plugin. This answer should also take into account things like readability, organisation of code and personal preference within a set of guidelines.
However, this all being said, I would keep common functionalities grouped together in either a plugin or a custom functions file which will be easy for me to remember later on where certain stuff are saved