If you do any business in California, you will have to pay the $800 minimum franchise tax regardless of where you incorporate. Note that Corporations do have a first year exemption from that minimum franchise tax. LLCs do not.
For NY, there is an expensive newspaper publication requirement, typically $500-$1000+ depending on which county your primary office in NY is in.
There are cheaper counties to publish in, but technically, your office should be in the county in question. Remember, this is on top of the NY minimum franchise tax (which is MUCH lower, yes).
Disclaimer: This post does not constitute and should not be relied on as legal advice nor does it establish an attorney-client relationship.