Phd advisor funding problem I am in the third year of my PhD. My advisor is very nice and he has helped me out so far in terms of my research, and other things as well. He is very approachable and we really bond very well. He even understands me a lot. 

The problem is that he does not have funding and never mentions much about it. Sometimes, I feel since he does not have money he tends to cut short the experiments or divert them. He mentioned about working on a molecule which I am not interested in but that is the only funding my co-PI has, and I have to work on it. He mentioned not to worry much about that as I will eventually get publications and graduate. I feel that my research is being hampered due to this and I am lacking behind in terms of data. 

Should I leave the university and look somewhere else?

This is my third year and it feels late to get into all this. Am I making a big deal out of it and should I just be thinking about graduating?
You should have a serious sit-down conversation with your advisor about your goals and interests, and talk about what the obstacles are that will need to be overcome. If you will not be able to work on something due to lack of funding, that is exactly something you need to be clear on if you aren't already.

If they don't have funding for the Project X you want, and only instead have funding for work on Project Y, you can A) ask what options they are aware of to get involved in work with something like Project X, B) ask for other potential alternatives beyond Project Y, and/or C) decide to try Project Y and maybe decide it works for your long-term goals (or not), even if it isn't what you had in mind originally.

As to the question, "should you just be thinking about graduating" - no, you should be thinking about what you are doing to do after you graduate, and how to use these years to contribute towards what you want to do beyond the immediate program. I don't know what you want long-term, and I don't know how Project X or Project Y fits in to that - but that's exactly what you need to find out for yourself. 

Things don't always go as we plan, so you'll have to remain focused on the big picture and be willing to be creative to find way to make what is available work for you. This could conceivably mean a different program, but it seems awfully early in the process to conclude that because 1-2 people don't have funding for one project you were interested in that you now have to change institutions. There could be other people, other projects, other labs - but the time to do that is before it's too late, such as when they are announcing you passed your defense and it's time for you to get out and take your diploma with you.