Running AC/MC cable in boiler room, do I need additional metal conduit?
This question may seem to be fairly straight forward but it is not and here is why. 

First in the NEC AC cable and MC cable are two different cabling systems and follow similar but different requirements. Since you have asked which one would be better, MC is permitted in more situations. AC is NEC Article 320 and MC is NEC 330. So you need to determine how exactly is your basement is used and if you are going to change it at anytime. Normally I would say either system would work fine in a normal basement situation, but if your AHJ believes it to be a damp or wet location. Then you will need to use MC. (See the articles for use permitted and not permitted). 

Second you are trying to find out the requirements of wiring a basement but you are not sure if it is finished or unfinished. Once again it depends on its intended use and your AHJ can help you determine exactly what you are trying to do. Some of these classifications are covered in Building Codes but not necessarily the NEC.

Third you are asking if you should run cabling in a conduit system. This is common for DIY'ers to think you need to run cabling inside of conduit, but a conduit system is an alternative to a cabling system where allowed by code. So let me suggest if you are going to run conduit don't put a cable in it just run the conduit and the necessary conductors and this will cost less and be a better system. Determine which conduit system you want to run NEC Articles 334 rigid metal, 348 flexible conduit, 352 rigid pvc conduit, 358 electrical metallic conduit, or 362 electrical nonmetallic conduit.

If I may suggest and as I have mentioned above, get in contact with your AHJ and he can help guide you through what you are going to need. I know some people think they are annoying and a problem, but my experience is they can be very helpful when you get them involved early. Remember they work for you and want to help you protect yourself from many different things such as safety and lets say shady contractors.

Good luck