If you are directly employeed by your employer, your employer will
pay EI and CPP. And you will have EI benefit after contract is
finished. But you won't have any other benefit, such as medical
expense, vacation (your employer should pay additional 4% after the
contract finished).
If they ask you to sign the contract as indepedent contractor, such
as incorportated, you take care everything for yourself. This happens
when you deal with job agency in most cases. You are not allowed to
pay EI, so you won't get EI after the contract. However, you can
deduct lots of expense when you file income tax, such as car expense,
meal, computer and Internet expense, utilities, rental, and many more.
But filing the tax is more complicated.
So it all depends and it is difficult to judge which one is good. When
market is good, I will choose the second one because I don't have to
worry about finding the next contract. When market is bad, I will
choose first one becuase I can have EI even if I can't find another
job after contract.