When I lived far south, I knew where to go: south to Kankakee to Blain's Farm and Fleet, or west to Frankfurt to Alsip Nursery. There were other places, too, but I had them memorized by location, not by name, so I'd simply drive to them.
Now that I'm in the city, I seem to be forever looking for a resource I really like. It seems nobody has everything in one place. Maybe that was true in the burbs, but I didn't notice it as much because I had a car and drove everywhere all the time anyway.
Here are the few places in the city I've found so far:
Gethsemane Gardens: (773) 878-5915 | 5739 N Clark St, Chicago, IL
Indoor plants, outdoor plants, trees, veggies, perennials, annuals, etc. They even have some furniture and some tools, but this is mostly for the plants. They have only one or two types of soil - and not one that goes in a self-watering planter. I have, however, purchased some lovely heirloom tomatoes. Their herbs are usually extensive. I've never seen any diseases or pests on the plants. Staff has been extraordinarily helpful when I've needed it.
Farmer's Market Garden Ctr - 4110 N Elston Ave, Chicago, IL 60618 (773) 539-1200
I've been in a few times, but always looking for something specific that they never have. They have basic potting soils in your major brands and carry a reasonable amount of plants in the spring - annuals, veggies, herbs. I didn't notice any heirlooms, but I wasn't looking. They also do landscaping, I believe.
Grand Street Gardens - 2200 West Grand, Chicago - 312-829-8200
Only went once. It's a small lot, but packed. For the size, they had more than I expected. They had some heirloom selections and a reasonable section of fertilizers and natural solutions (soaps, greensand, etc.). I can't remember what I bought there, but it was the only place I'd seen it in the city. I paid about double what I remember paying in the burbs, but alas, that is the city.
Fertile Gardens - 1650 W Diversey Pkwy, Chicago, IL 60614 (773) 929-9330
Definitely not low priced, but no higher than Gesthemane, they do have a good selection of heirlooms and some varieties you don't see at some of the other places. Things seem well taken care of. Again, not much, if any selection in soils, amendments, fertilizers and the like. While not rude, most staff seems more focused on plants than on communication, but that could just be my experience. It's certainly a nice place to go if you don't want any staff interaction.
The only other place I've been to is a temporary structure in Menard's parking lot (on Clybourn). They have your basic flowers, both annual and perennials, along with some veggies and basic herbs. Not a huge assortment, but decent, and with good prices. I even found a couple heirloom tomatoes there last year!
Places in the burbs:
Meinke Garden Ctr-5803 W Touhy Ave (between Lehigh & Mason Ave), Niles, IL 60714 (847) 647-9455
They have many greenhouses and a pretty decent herb collection. They sell some tools and soils, but the focus is plants. Not sure how many perennials, as I've usually been looking for veggies and annuals or herbs when I've been there. Not much in the way of heirlooms, but mostly your standard stuff. Do inspect your plants before purchase for whiteflies as whiteflies are notorious in greenhouses.
Pesche's - 170 S River Rd, Des Plaines, IL 60016 (847) 299-1300
I've only been once as it's not close to me. It seemed large, but it was already a bit late and they were out of most of what I was looking for, so do get there early. They did have Korean cilantro, which may or may not have been culantro.
Alsip Nursery - Route 45, Frankfurt, (a bit north of Route 30)
They have a lot of other stuff, but a pretty good selection of gardening supplies, tools, plants, trees, etc. It was usually one of my go-to places when I lived out that way.
In the city, I'm still looking for places that have a good selection of organic and natural potting mixes, fertilizers, additives, etc. This is the stuff I usually end up ordering from Garden's Alive, Gardener's Supply, or other catalogs. I don't want to pay shipping for much of these things, but seem I must when I can't find them locally.