Boots vs. shaft replacement...
If your cv's are in good shape I would do the boots UNLESS the shop is replacing the shafts with OEM shafts.
Aftermarket shafts are no where near as good as the OEM shafts. On that note the best aftermarket shafts I have found are the Empi's. They are good but still not the quality of the OEM's. At the cost quoted you I am almost certain you will not be getting OEM. Just my 2 cents.