Phoenix
For more options see the link below. Happy Holidays 
-Glen
Flagstaff
-------------
Travelodge Suites
2755 Woodlands
Flagstaff AZ 86002
520 773 1111
Motel 6 West
2745 S Woodlands
Flagstaff, AZ 86001
520 779 3757
Holiday Inn Flagstaff
2320 E Lucky Lane
Flagstaff, AZ 86004
520 526 1150
Residence Inn
3440 N Country Club
Flagstaff, AZ 86004
800 424 4777
Sedona
-----------------
Desert Quail INN
6626 St. Hwy 179
Sedona, AZ 86351 86351
800 385 0927
John Gardiner's
525 Boynton Canyon
Sedona AZ 86336
520 282 2900
Matterhorn Moter Lodge
230 Apple Ave
Sedona AZ 86336
520 282 7176
Quality Inn Kings
771 SR 179
Sedona AZ 86336
520 282 1533
You could try some of these, a few offer cabins etc. and look very nice. Results of yahoo search; "sedona az. lodging pets"
This is from the first listing , there are other guides available.
Happy hunting!
1. Sugar Loaf Lodge
(928) 282-9451
1870 W Highway 89a
Sedona, AZ Map Rate this 1.90 mi
... Restaurants Private in-room baths Air Conditioning and electric heat in all guest rooms Pet Friendly Pool and Whirpool Scenic Views Close to Hikiing and Mountain Biking Trails Shopping,... more on web site
Category: Hotels and Motels - Other Lodging
www.sedonasugarloaf.com
2. Sky Ranch Lodge
(928) 282-6400
1105 Airport Rd
Sedona, AZ Map Rate this 2.09 mi
Category: Hotels and Motels - Other Lodging
www.skyranchlodge.com
3. Matterhorn Lodge
(928) 282-7176
230 Apple Ave
Sedona, AZ Map Rate this 0.14 mi
...Senior Citizens (62 years) receive 20% Discount off regular rate on first nights lodging. 20% Off Regular Rate...Limited pet rooms available... more on web site
Category: Hotels and Motels - Other Lodging
www.matterhornlodge.com
4. Super 8 Motel
(928) 282-1533
2545 W Highway 89a
Sedona, AZ Map
2 stars out of 5 stars
Rate this 2.56 mi
Category: Hotels and Motels - Other Lodging
www.sedonasuper8.com
5. Sedona Real Inn
(928) 282-1414
95 Arroyo Pinon Dr
Sedona, AZ Map
3 stars out of 5 stars
Rate this 3.20 mi
Category: Hotels and Motels - Resorts - Other Lodging
www.sedonareal.com
6. Oak Creek Terrace Resort
(928) 282-3562
4548 N Highway 89a
Sedona, AZ Map Rate this 3.69 mi
Category: Hotels and Motels - Other Lodging
www.oakcreekterrace.com
7. Best Western Inn of Sedona
(928) 282-3072
1200 W Highway 89a
Sedona, AZ Map
3 stars out of 5 stars
Rate this 1.33 mi
Category: Hotels and Motels - Other Lodging
8. Holiday Inn Express Sedona
(928) 284-0711
6175 Highway 179
Sedona, AZ Map Rate this 5.73 mi
Category: Hotels and Motels - Other Lodging
www.sedonaholidayinn.com
9. Bell Rock Inn & Suites
(928) 282-4161
6246 Highway 179
Sedona, AZ Map Rate this 5.82 mi
Category: Hotels and Motels - Other Lodging
10. Desert Quail Inn of Sedona
(928) 284-1433
6626 Highway 179
Sedona, AZ Map
2 stars out of 5 stars
Rate this 6.34 mi
Category: Hotels and Motels - Other Lodging
www.desertquailinn.com
Iris Garden Inn
(928) 282-2552
390 Jordan Rd
Sedona, AZ Map Rate this 0.19 mi
...We welcome everyone, including your pets (click for pet policy) , to an environment of relaxation and rejuvenation at a discount... more on web site
Category: Hotels and Motels - Other Lodging
www.irisgardeninn.com
12. Quail Ridge Resort
(928) 284-9327
120 Canyon Circle Dr
Sedona, AZ Map Rate this 5.55 mi
Category: Hotels and Motels - Other Lodging
www.quailridgeresort.com
13. Motel in the Pines
(928) 286-9699
80 W Pinewood Rd
Munds Park, AZ Map Rate this 8.05 mi
Category: Hotels and Motels - Other Lodging
14. Lo lo Mai Springs
(928) 634-4700
11505 Lolomai Rd
Cornville, AZ Map Rate this 10.00 mi
Category: Hotels and Motels - Campgrounds - Mobile Home Parks - Other Lodging
www.lolomai.com