I have Minecraft on my computer as well, and when its running it uses a lot of the system resources. The game uses your RAM heavily becuase it wants to store all the game data it can in active memory so that the screen can be updated as you move with out lagging so much. It is normal for the game to consume >90% (greater than) of the processsor becuse it's constantly having to deal with I/O from the memory. I believe it has to do with the game being programmed with only Java, Java is resource heavy anyway. I don't think its a problem with your computer it's just how the game is. Version 1.9 of the game is the worst about that problem. I tried version 1.1 and while it still has some heavy use, at least it don't stay at 99% cpu usage all the time like 1.9 did.
I have the game open and running now, it's keeping the CPU at 92% and it's just sitting there paused with RAM usage at 1.1GB of ram just for the Javaw.exe process. So I don't think its a problem, its more of a "because it is the way it was made" issue. I have an AMD Phenom II X2 and Minecraft keeps it busy to say the least.