I need to send serial data over a very noisy channel with lots of attenuation. I was thinking of using Manchester coding. However, the difficulty would be in designing the receiver. Since, I'm not that experienced with analog can anyone recommend the best way to recover the signal?

I was looking at using one of the Cypress PSoC series, as it also has some token analog functionality.
http://www.cypress.com/?id=1353

 

The usual way to do clock recovery is to introduce code violations before the actual data. There are many other tricks to using Manchester encoding and they are the subject of whole books.