In-content links - better?

Yeah but that was a yahoo spokesman.
Google is focusing more on latent semantic indexing  nowdays.

Either way probably wont make a huge difference, and no harm in doing both.
Personally I like header and footer menus myself though, just for ease of navigation.

Design your menu placement for your visitors and it will probably end up working well for google as well.
Google tries to get the most relevant and user friendly sites ranking, so make your site like so.