Shall you use one of these, according to Oxford Dictionaries Online, you should only use an apostrophe "for the sake of clarity", therefore opting for the first option ($x_i$s).
There are cases, like this in Statistics, where you can use the plural, for example, for a variable as the p value. You would then write ps to show the use of multiple p values.
However, these are different variables, with possibly unrelated calculations (even though the formula is the same). In the case of a sequence, xi$x_i$ is already a generic term, representing each element or the sequence itself. You can then write:
- "the sequence $x_i$", or
- "the sequence $(x_i)$"