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.

As a first choice separate crowns are a better option. Its easier for you to clean and floss around them. If one or both teeth is weakened from the decay, joining both crowns together would be advised.

Dear acjs: There are only a couple of very specific reasons to connect two molar crowns.  One is loose teeth which need to be splinted due to periodontal disease.However, by enlarge, connection of teeth IS NOT recommended or desired.  A "stand alone" crown will outlast connected crowns without a doubt. Unless there is a specific reason as to why the crowns should be connected, they should not be.Please talk to your dentist about it.

It is much better to have individual crowns. If you have two adjacent crowns that are joined, then there is no maintainability as far as hygiene is concerned. No matter how well you try to clean under two fused crowns, inevitably you will develop caries (dental decay) or gum disease in the area.