It depends.
Filing as Married Filing Jointly usually provides the greatest tax benefits of the higher standard deduction and lower tax rates.
However, both of these states do give you the option to file separately for state purposes. Since you have a different residency period for PA, you will be able to file separately there.
Generally, in California you need to file using the same filing status as you use for federal purposes. However there is an exception if your nonresident spouse does not have any California source income. Since this the case for you, you would be able to file as Married Filing Separately for California.
See the following link for instructions on how to prepare the Married Filing Separate returns for the states. You will need to create mock state returns using the instructions in the link below You will need to mail the state returns in as well.
How to File MFJ for Federal but separately for state
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