You can try the expat-owned Hostal Aqui: http://hostalaqui.com/ — if nothing else, they will be able to tell you where you can stay with your pet. (They have dogs themselves so not sure how yours and theirs will get along). Another I’ve heard accepts pets is Hotel Coco: http://www.cocos-hostal.com/cnt/index.pl?cat=4&lang=en
I’ve not stayed at either place so can’t tell you what they’re like. I have stayed at Hotel Amira, though, and you might inquire about their policies: http://hotel-amira.com/ You can either write to them in English or try your hand at Google translate or another internet translation package.
Any of these hotels should be able to arrange transport for you. Be sure to tell them you will need a van and not a taxi.
An English-speaking driver that has been recommended to me is Will Rodriguez: willienavy70@gmail.com; cell: 098-699-2334.
From the US, you’ll call 011 593 98 699 2334. I’ll find you another driver or two as well — watch this space.