What kind of broker is your wife? CRE? CRE 101 - if the appraisal comes in lower than the contract price, negotiations should be started on a price credit. You really need someone with CRE experience in your corner(maybe your wife can partner with an experienced CRE broker and split the commission).
Those NOIs don't add up to the contract price you have agreed to. Your working at a 9.3 multiple at best to 15.5 multiple at worst on reported NOI. Cash the owners have taken out is not verifiable and thus is not factored into the sale price. They didn't report the cash and that is their reward, they can't then expect to have that unreported and unverifiable income counted towards the sale price. Tax return income is what counts, if those look fishy, ask to see the IRS tax transcripts. Remember this is a business
transaction and should be treated as such. Everything the sellers tell you has to be verified.
Also, are you going to be able to cover the debt service and have an acceptable return on your money afterwards? A rough calculation would put your debt service on that contract price loan between $25-30k a year or more depending on your int rate, which would come directly out of that NOI.
Is the lender a bank or a secondary market lender? I have never had any issues getting appraisals from the lender for review before closing, as you said you paid for it. You need to see it and study it - most good appraisers will include their opinion on the location, area, and future of the area. How much did the RE value at vs how much did the biz value at?
Again, not trying to scare or deter you. This saying holds true always - its better not to have a deal than to have a bad deal! A lot of people will try to push a deal through because they have so much time and money into it already. If the deal doesn't make sense as you dig further into it, don't be afraid to cut bait and walk away to fish for another deal. Getting a bad deal as the economy turns south might be one of the worst combinations.