PhD funding for only 4 years
I don't think getting 4 years of funding is necessarily a red flag all on its own - the amount of funding you get offered will vary widely both between schools and between fields.  I think there are three things for you to consider:


Non-financial issues.  How good is the school, where is it located, and most importantly, how good of a fit is it for you?
If all else were equal, offering more years of funding is (obviously) better than offering less, since it gives you more time to work.  Even if you don't think you need it now, it's still a benefit in the form of lower pressure, and padding in case something disrupts your work (illness, research setbacks, etc).
Offering you better funding is potentially an indicator of how much the program wants you there.  That is, the program offering you 5 years of funding (with a possibility of 6 even), is signaling their interest in you quite strongly, while the program offering only 4 less so.


The problem is how to compare number 1 to numbers 2 and 3.  What are the merits of the program offering you 4 years of funding?  If there's a strong non-financial argument in their favor, maybe ask the department to put you in touch with some of their current PhDs and recent graduates.  Ask what the program is like, ask if they offer 4 years of funding to everyone, and ask how practical they find that deadline to be.  At least in my field, this was a fairly common occurrence for prospective students.