Pretty much a tossup. You are getting a 10% premium on the 1099 which covers your SETaxes. The 1099 would also make it easier for you to deduct business expenses. You would also have to look into voluntary SDI (State Disability) if that was something that you want in case of an injury or family leave. (This will depend on your state as well).
Is this being offered by the same potential employer? If so they can't arbitrarily choose which classification to put you under.
PiratesSayARRR is right. There is a legal (albeit somewhat fuzzy) definition of what a sub-contractor is and if you don't fit it you can't legally be paid as one lest your employer get fined if they're caught. Any disgruntled current or former employee/"sub-contractor" could anonymously blow the whistle to the IRS. That's potentially a pretty big risk they're taking on, especially if you're not the only one they're doing this with.
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