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

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.