MySQL with high CPU and memory usage
There is something you are not taking into account.

MyISAM caches index pages into the Key Cache
InnoDB caches data and index pages in the Buffer Pool
I wrote a post about this : What are the main differences between InnoDB and MyISAM?

The 466092032 you gave is just the number of bytes taken by indexes. The InnoDB Storage Engine is moving data and index pages (each InnoDB page is 16K) in and out of the Buffer Pool due to its small size and the amount of data you are not accounting for.
Please refer back to my post. It will recommend how to size both key_buffer_size (which should be about 84M in you case) and the innodb_buffer_pool_size.
RECOMMENDATIONS

Increase the VPS RAM enough to fully accommodate your data.
Lower the read and write threads since you are in a VPS
Disable the query cache because it slows down InnoDB : See my post Is the overhead of frequent query cache invalidation ever worth it?