Flowers can be mis-interpreted leh...i always think it's appropriate for a guy to give only give flowers to either a gal he fancies, or to gf, or to mum, or given by gal to gal (e.g. I would find it strange if my partner gives them to another gal).
How about giving a nice gift hamper - can get from the florist or gift shops (not those huge hamper with cognac type lah ). Or give branded cookies/snack hamper, more neutral....assuming this is a neutral r/ship.
I think depends on your boss's character and age. If she's quite senior I'm sure she won't misinterpret your intentions. I have also received flowers as bday pressie from a platonic male friend. It really depends - don't court danger if your ex-boss is on the lookout for romance, of course...
Some choices for you to consider...normal and low budget ones to choose from: