After having roots canal on two molars would it be best to have joint crowns or two individual ones?

I would leave the crowns separated to allow for you to floss thorough them.  In addition,  this would keep each tooth from having extra forces placed on them when splinting them together.  You would get more longevity by keeping them separated. Good luck.  

Unless your teeth are mobile (slightly loose or "wiggly" from loss of bone cause by periodontal disease) splinting (joining two or more crowns together) is usually contraindicated.  Splinting makes cleaning your teeth much more difficult, and thus oftentimes actually causes gum inflammation and irritation that could be uncomfortable to you.

If the bone support of the teeth is good then I recommend keeping the crowns separate. This will allow much easier cleaning and maintenance. Also in the future if something happens to one crown you will not be locked into treating both teeth.