We have been to Mexico City (loved it!) and will be returning in February.
This time we want to spend about a week in both San Miguel de Allende and Lake Chapala.
Can anyone recommend small boutique type hotels similar to Ignacia Mexico City?
Which locations are the best for interesting things to do?
Tips in terms of what things to do/what not to bother with/best ways to get to either location from Mexico City?
Any and all advice appreciated.

I would highly recommend Casa Calderoni in San Miguel. Charming B&B in a great location. Luxury Bed and Breakfast San Miguel | Trip Advisor Excellent Rating

In Lake Chapala, Casa Flores in Ajijic. Small and also charming.

Thank you.
Great tips as always.

Having lived in San Miguel for some 8 years, (but will probably be returning), I'm not terribly familiar with hotels in the price range of Ignacía (other than by location and reputation, or maybe their restaurant). But the following come to mind, in no particular order:
Doce 18, just half a block off the jardín. Upscale food court/shopping on site, and San Miguel's oldest still operating bakery across the street.
Dôce18
Casa 1810.
https://www.tripadvisor.com/Hotel_Re...ulf_Coast.html
Belmond Sierra Nevada:
https://www.belmond.com/hotels/north...usiness&cr=csn
And, while not necessarily considered 'boutique', the Rosewood is a fabulous property with arguably the best rooftop bar in town:
https://www.rosewoodhotels.com/en/san-miguel-de-allende
As far as things to do for a week in San Miguel, it all depends on your interests. There are a number of day trips easily made from SMA, some worthy of an overnight. A minor ruin site. Horseback riding. Over 100 art galleries. Just depends on what you want and your budget. And of course, plenty of restaurants in all price ranges.
As far as Chapala, I have limited experience there. But from what I do know/have seen, I can't see spending a week there unless you're scoping it out as a retirement location. Or are willing to travel to Guadalajara often. I think you'd be better off to subtract some days there and spend time in Guanajuato and/or Queretaro.
As for getting to San Miguel from CDMX, you've got a couple options. You can hire a private, door to door shuttle service such a Bajiogo. Expensive. 2 bus lines leave the Norte bus station, ETN, and Primera Plus. The former has more daily departures and double-decker buses, but they make 2 brief stops (Tepotzotlan and Queretaro) on the way with no bus changes. Primera Plus is direct, fewer departures, no stops. Both are super comfy with wifi.
I will also add that Casa Calderoni is a popular place, run by long-time San Miguelenses in a great location, right across the street from a great coffee shop/breakfast spot popular with local expats.

We took a bus to SMA from Mexico City. I would say you need some knowledge of Spanish to figure this all out or use Google translator. I don't speak Spanish and I don't know where I would have ended up if my travel partner, who does speak Spanish, had not been with me.

We discovered a small hotel while we were there- did not stay at it, but very cute with small restaurant. Hotel Petra. Great location, We spoke to a local who was staying there while he rented out his much larger home. He recommended it as a place to stay- this is not a 5 star hotel by any means but looked comfortable.

Thank you for the specific information.
I referenced Ignatia only because we like the quiet peaceful charm of the spot and the lovely location and design. We do not necessarily need the price point but perhaps one goes with the others. We have also stayed at The Red Tree in Mexico City and while it gets top notch marks for the hospitality of the hosts the evening ambiance at the happy hour became monotonous with the chronic talk of the affairs of the American political situation. To that end we are looking for a smaller quieter spot.
Your suggestions are most appreciated and we are thinking exactly as you suggest in regard to Chapala. Perhaps a week is too much.
Always appreciate the support of the Fodor Forum readers.
Thank you.

Look at La Casa del Parque. We have stayed there 3x and love the quietness. Breakfast is included and her gardens are peaceful. It is not far from El Jardín. Eat at 1810. We had two great meals there and the sevice was great. Enjoy your trip.

Are you going to both San Miguel de Allende and lake Chapala for one week? I'm looking for such a trip but thought one week wasn't doable...
How are you doing this?

(bellatravel) You asked about Mexico City and Oaxaca or Puebla... entirely different two places than SMdA and Lake Chapala.