I am looking for a company(s) that will produce a prototype toothbrush
for me. I would only need about 5 of the brushes. My prototype is not
the same size or shape as a regular toothbrush, but a toothbrush
manufacturer would do just fine.
I also would like to know the estimated cost to produce the 5 brushes.
Preferably the company would be U.S. based.

I'm not certain how toothbrushes are made, but I'm pretty sure that
the handles are made from injection molding. If so, then you would
either have to use an existing die to make the handle or have a new
die made. A new die will cost $10,000 to $50,000. Then you'll have to
find someone willing to make it. That requires a manufacturer with an
injection molding machine. They'll lhave to charge a setup fee to make
such a small number of items. I'd
estimate that will cost $2500 to $6000, but probably toward the lower end. 

One thing that might help a researcher to answer your question is to
know if the handle design or bristle design or both are unique to your
prototype. Also, what are you going to use these for? If you plan to
present your idea to a manufacturer or investor then I would suggest
that you start with a drawing or clay model. If you can't draw it
yourself, you can make a sketch and a graphic artist can draw it for
you. The cost should be $75 to $200 for an independent graphic artist.

If youy prefer a clay modle then check at the local college for a
student in their art department. I'd guess that you could get student
to do it for a reasonable fee.

Hope this helps.

Can you create the prototype from an existing brush?

Does it need to be functional or just pretty?

For just 5 brushes of a new design, I would look to a model maker.
- at a guess they would use a form of resin

Incidentally injection moulding costs have come down, 13 years ago I
heard that they were making 'multiple' moulds, eg: one mould that
contained a load of other small bits. The cost implications were
considerable.

Also CNC and CAD technology has simplified things.

For 5 prototypes you would NEVER mold it they way you would in
production.  It would be far smarter to "hog" or carve them from a
block, and insert the bristles by hand.  Once the concept proves out,
the design is "frozen", the market research is done, the funding is in
place, and the project gets the green light, at THAT point it would be
appropriate to go to the expense of making a mold. 
http://www.flex-partners.com/  can help with all aspects.

Big Blue