We are heading to Namibia at the end of September. I did a bit of research a while back and heard great things about The Stiltz in Swakopmund. No availability for the time we are there, but it would have been my choice.
http://thestiltz.com/
We ended up booking at The Strand Hotel in Swakopmund. Newer, probably a more typical hotel experience, but it's on the water and was well reviewed.
Enjoy your trip! I know we are looking forward to Namibia.