Please find attached a paper where combined DAPI and SYBR green staining was used for bacterial biofilms in sediments. This method will allow to distinguish true bacterial signals from background noises.
If you got access to Laser Scanning microscopy, this would be definitely the best way to obtain representative counts.
If you want to produce mono-specific biofilm using a bacteria which is not difficult to grow on agar standard media, cultural methods remain a good option. This is not necessary the best way but you could have good estimations at low cost, moreover few equipment are needed. If you are interested I can give you an example of procedure.
You can swab the biofilm using a sterile cotton swab and transfer it into a sterile test tube with isotonic saline. Then make appropriate dilutions and spread plate it. You will get accurate results.
At least you have two options for biofilm measurement, CFU counting and resazurin assay at 560 nm. these techniques are very cost and time effective.
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