I don't think your main issue is around starting a project, seeking funding, and bringing in a new student -- In fact, there's an argument to be made that this is not really your business (I wouldn't argue that, but there are those, some of whom know what they're talking about, that would)
What you're really concerned about, without really saying it, is your intellectual property rights. If you're an inventor, you need to be listed on any patents as an inventor -- even if there are other people who also should be considered inventors.
It's a delicate issue to broach, and frankly, even bringing it up can have unforeseen ramifications and impact the relationship with your advisor. The fact that your advisor has a company and financial interests complicates this further.
So, if I were in your situation, what would I do? Once I decided that pursuing it was better that not pursuing it (and the latter is certainly a real choice, and the easiest choice), I would probably approach my advisor and say something like "I believe my contribution to Substance Zeta might be sufficient to make me one of the inventors of Substance Zeta, and I'd like to meet to discuss our intellectual property scenario".
The response to that would pretty much define your further response. You might get a "you're completely right -- let's apply for a patent", in which case you'd go to whatever mechanism your university provides for these things, often some office in charge of technology transfer, and start the ball rolling. Your prof may instead want to do this independently through his company, including you as an inventor. This may or may not violate their employment terms.
If you get any real reticence, you may choose to drop it, or you may choose to pursue it further. The latter may start a S--t show. (In fact, just bringing up the subject in the first place might also, but if you're dealing with a mature level-headed person, it shouldn't).
There are a variety of responses to reticence on your advisor's part. Possibly the most effective one would be "Because of the financial interests involved, I feel there may be a conflict of interests on both our parts, and I'd like to use university mechanisms to establish a conflict of interest plan moving forward. Perhaps we should schedule a meeting with the Chair".
I think a mature investigator may respond "you know, you're right -- let's do that", but there is a real possibility of starting up a s--t show, and the response could even be "get out of my lab". Degrees have a tendency to go away in s--t shows.
Before starting any of this, you probably want to review the whole situation, and think about whether your contribution is actually provable. If it's not, I'd lean toward dropping the matter.
As a disclaimer, I am not a lawyer, and even if I were, you're not my client. The way to really make sure your legal interests are well-covered is to hire a lawyer.
UPDATE: The reason why I say the IP is really what you're interested in is because if the IP is handled correctly, you really have no worries about what happens next. At the very least, you'll get recognition as an inventor (based upon what you say in your question -- of course, your mentor may see things a whole different way) and presumably a portion of the financial fruits if something turns this material into a windfall, or even if it just gets licensed. In fact, it's conceivable that your mentor's company may have to license the use of the material from the university.
To back up Dr. Krause's excellent answer, yes, people with the most money to either back up or tear down a patent often win patent cases. One of the easiest ways to void a patent, though, is to prove that the inventorship listed on a patent is wrong. If your contribution is as central as you say it is, and if the material has real commercial promise, then it is in everybody's interest to make sure that the patent goes in with the correct inventor list -- your interest, your boss's interest, his company's interest, and your school's interest.