The spatial index, as with other objects, have their own
script <object> as menus and need to be done separately. This can be done to the clipboard and pasted to the query window generated by the
script table as command.
I can't confirm at the moment, but I suspect that the primary key and other constraints come out in the
script table as options since the are an integral part of the table definition, whereas indexes are not.
generate and publish scripts wizard can also be used, but it is a lot of steps if you are just doing a few items.
Technet, How to: Generate a Script