We bought a van in Canada to roadtrip the US for 6 months. We are planning on two 90 day stints in the US so as to comply with the ESTA requirements. It is looking more likely it will be easier to fly Mexico rather than re-enter Canada via land. Will customs have an issue with us leaving and re-entering the US via air if we originally entered via land border? We have done the west coast and want to now travel the East coast. Thanks.
The simple fact is, you're very likely to have problems.
What you are describing is very clearly a "Visa Run", and even if it's technically within the rules of what is allowed under the VWP (and whether it is or not will depend on the exact details, many of which you haven't provided), there is a very real chance that you will NOT be allowed re-enter the US on your second attempt if the immigration official decides that you are doing a Visa Run.
Instead you should likely apply for a US B-2 visa which will allow you to stay in the US for up to 6 months at a time.