The prices you will be quoted for a transport to the Gili Islands (in Ubud anyways) will be outrageous.  All the brochures quote 660,000rp (about $80) each way, or 1,200,000rp return!!  If you haggle hard, most of the travel agents in Ubud might give you 100k or 200k off, but won't come much below this price.   A travel agent on the north end of Monkey Road (on the left side) called "Alit Shop", sells tickets with the company Ekajaya (most travel agents use this one as well) and his starting price was 400,000rp/person one way.   A return ticket can save you even more money, especially if there is two of you, expect to pay about 700,000rp per person for a return ticket.  Some hotels also sell tickets and might be more willing to give you a fair price.   Each company has it's own vans to shuttle you to the port town, but Alit Shop will put you on a separate transport company (Gora), maybe that's why the tickets are cheaper.  The van will drop you right in front of the Ekajaya office in Padang Bai where you will receive you boat tickets and then escorted to the boat, the whole process is very streamlined.

 Also, there is a lot of confusion as to which companies and boats actually go to Gili Air.  Most only go to Gili Trawangan, although the story will differ between travel agents.  The companies that for sure go to Gili Air (directly) are Gili Gili and Ekajaya, though there may be more.  The boat stops first at Lombok (unless none of the passengers are going there), then Gili Trawangan, then at Gili Air.  Otherwise you would have to take another boat (about 25,000rp) from Gili T to Gili Air.  The return pickup can also be from Gili Air.

 Hope this helps.