This is very dependant per mangaka. And all tough there is a thriving independent market for manga, it is rarely a solo effort. Hence most of the mangaka start off as either an assistant, or manage to get a contract at a well known publisher. Now, as for how much they earn, lets take Eiichiro Oda as an example. He has been estimated to earn around 2 billion Yen($~24 million) based on royalties alone.
Now how is this amount built up?
Contract and Royalties
Most mangakas don't earn an hourly wage. Instead, they have a contract based employment with partial sales (royalties) agreement. This means that a mangaka makes XX amount of pages per month for a set price. For a starting mangaka, this is around 500$ for 20-40 pages. On top of this, they still earn their royalties, which is around 10-15% per tankobon. These tankobons sell around $5 each which would make ~$0.50 a tankobon. Given that it takes around 5 hours for a page, we can say that an average starting mangaka earn about 5$ an hour.
This brings me to the pretty well known fact that mangakas tend to have a second job. As for a starting mangaka, it is not sufficient to pay the bills.
Series becomes an anime
Lets say the given manga became a success, and became well known enough to create a anime. This would mean that our mangaka gets roughly ~$660 per episode. So a standard 1 cour anime would earn just under $8000. But they do not get royalties for the DVD/BD sales. The royalties for these go to the sponsors and publishing companies. Most of the time the mangaka does not even have a say in the production of the anime, and the anime is only made to promote the original series and earn the publishers/sponsors money.
Character goods
Now another profit factor for most mangakas is the sales of character related goods and products. Most of the time, this is also covered in the same contract as mentioned above, meaning that the mangaka also earns 10-15% of the remaining anime retail, as most of these products tend to be a lot more expensive.
Character goods earns around 8.5 times more then sales of movies, DVD's and VHS combined based on the American market in 2009
TL;DR
It is estimated that a mangaka earns about 10% royalties over their product sales, excluding DVD/VHS/Movies/BD. Leading to ~$0.50 per tankobon and ~$0.05 - $20 for product sales such as figurines, key chains etc,etc.
Which, for successful mangakas, can turn up as high as 2 Billion yen (1.29 Billion tankobon royalties, 749 million character good royalties).
Sources: crunchyroll, AnimeNewsNetwork, Yahoo Answers, several Wikipedia pages.
