I have never seen a company selling new engines without a swap, but I haven't been in this sport all that long.  I am pretty sure that BRP-Rotax is not still producing the 947/951 engines.  That is why most, if not all, companies require another engine to swap. So you may be outta luck.  You'll have to see if someone else knows more than me and can provide you with a company that you can buy one from. 
As an alternative, you may want to look on craigslist or ebay for a used motor or a damaged ski for real cheap.  You may find a usable motor you can just stick right in, one you can swap for a new rebuild, or rebuild yourself.
  
I think without a core to swap/trade, even if you were to find a company that would sell you one, you are going to be paying thousands of dollars (2k-4k).
You may even find a ski in better shape than your own.  As an example, I just bought a 98 GSX Limited with only 39 original hours for $2400 with a trailer from Craigslist.  If I wanted, I could have pulled the engine and parted out the rest, probably making most of money back.
Good luck.