I've looked through Arsenal and I've searched here but can't find this one. I've got how much parts cost for mods and repairs, but not rates to pay someone to do it. Assume that the character does not have a mechanic contact, but its a legal mod to a legally-owned vehicle tagged to a legal SIN; what's this going to run me? (Should it be a percentage of the parts cost or should it be based on the successes required?)

In Shadowrun Missions a Mechanic gets 100nY per hour, each test interval is 6hrs long.

How do you determine how many dice an "average" mechanic gets, and shouldn't the rate be determined by the dice pool (otherwise the least skilled mechanics-- the ones that take the longest-- will also be the highest paid)?

The least skilled mechanic wouldn't be payed at all, since his dice pool isn't high enough to complete the job

3 Attribute, 4-6 skill, equipment bonus such as AR plans, and teamwork. It probably wouldn't be a single mechanic but a garage. Depends on the damage, of course

Of course, in addition to the 100¥ per hour (which is, in my opinion, overly simplified, but works out fine if you don't want to micromanage such things) you'll have to pay for the mod itself, too.

I've always used the mechanic contact in SR4A (pg 291) as an 'average' mechanic as he has enough skill to be actually useful. Guys with a low skill are more likely to be apprentices to someone with a higher skill, rather than working on their own. A guy with a 1 skill is a hobbyist at best.
If you wanted a guy who was more skilled than the mechanic contact then you can charge extra for his work, maybe 50% again over that 100¥ an hour. Less skilled mechanics could charge out at less and hope to make up the difference in the extra time it take to do the job.

So it looks like a 12 pool mechanic would be a reasonable assumption (pool+plans+teamwork for a functioning garage), which could buy 3 hits per interval (6 hours), so it would be 600ny per 3 threshold or more simply: Threshold x 200ny.

The only flaw I see with that is the lowest threshold I see is 4, which means even the simplest mod would cost a minimum of 800ny in labor. Likewise something like a standard winch (600ny for parts) would cost 2000ny in labor to have put on. (These are clearly what I would call "dealership prices".) I think it would make sense to have a modifier based the Tools requirement, because a repair or modification that requires only a kit to make would be simpler than one that needs a facility. Without really thinking it through, my from the hip numbers would look something like:

Repair Mods: Tools/Cost
Kit: Thresholdx50ny
Shop: Thresholdx100ny
Facility: Thresholdx200ny

There are still a few head scratchers (it seems like a competent garage could get a winch attached in fewer than 18 hours of solid working).

Honestly though Parts Cost + 30% would be simpler.

This is roughly what our house rule is. It takes the actual skill into account (5% per skill point with a mod based on the tools 5%/10%/15% respectively), so the simplest mod has labour costs of 30% using the Mechanic contact. If the GM is feeling mean or we've earned too much money he might apply that percentage for every interval. Much like in the real world, this can result in labour being more than the parts. Realistic in many ways actually.

Solution: Have your Magician sustain an Enhance Logic spell on the mechanics for the day. Blast them all up to their augmented maximum, turn them into temporary geniuses who can work on cars with the speed of an Indy pit crew, and they do your job at the start of the day for free. Their payment is that they get to clear all their other jobs fast and charge their other customers whatever the hell they want.

That makes sense to me... about 100/hr... 800 a day... 4000 a week... 16000 a month... going up to about 20k for 10hr workdays...

Take out taxes at about 40%... ~10k-14k leftover. Minus expenses for things like access to AR plan databases for servicing vehicles (probably a monthly fee to keep up with new models)... however much they need to pay for ongoing security costs... utility bills... hazmat fees for things like hydralic fluid and waste oil... amortizing the cost of tools and facility loans... after all that... looking at take home of about 5000... for a solid mid to high lifestyle depending on how long and established the garage is.