"We are talking about Internet router here. this will just be another router .. only special thing is the location (i.e. space)> I guess it will use BGP as all the other routers in todays Internet."
How many paths out will this router have? If it's only one or two, statically route it or use a couple of differently weight static routes and IGP wouldn't make much sense in most likely scenarios, maybe with NAT if a few nodes are going to access it.
If an IGP is necessary (if there are eventually several "space routers" and a few paths back to earth, EIGRP would make most sense, since Cisco is providing the hardware (EIGRP is a Cisco proprietary protocol) and EIGRP provides the most knobs to tweak to overcome latency and modify routing announcements.
BGP would only make sense if more than one ISP ends up providing connectivity in space (so you can easily multi-home) or we end up with several space agencies up there. We can't share an IGP with the ESA, JAXA or RKA.
