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This is a comparison between the two main contenders in the 16bit home computer era.

Since I was an Amiga user during this time I didn't have much on hands time with the Atari but I've researched a little and tried to compare the two platforms as unbiased as possible.

The prices are rough estimates of each systems individual launch prices. Special offers, reductions and different prices in different countries will mean that price ranges will vary.

Amiga 1000

1st generation Amiga (OCS)
MSRP 1,300$

Atari 520ST

1st generation Atari
MSRP 600$
68000 7.14Mhz CPU 68000 8Mhz
Memory 512KB RAM
12bit 4,096 colors Available Colors 9bit 512 colors
320×256 64 colors Most Colors 320×200 16 colors
640×512 16 colors Highest Resolution 640×400 2 colors
8bit 27kHz PCM 4 channels Audio FM 3 channels

Amiga and Atari ST were launched in the same year with the Atari ST slightly in the lead regarding price and cpu performance. The Amiga set the reference for graphics and sound and kept it for a long time. This came at a price, because of all the custom chips, putting the Amiga 1000 outside of the budget of many enthusiasts.

Atari 1040ST

1st generation Atari
MSRP 800$
Memory 1MB RAM

Atari improved their computer slightly by adding the Atari 1040ST which has twice the amount of RAM. Commodore basically had to acknowledge that an Amiga with 256 KB of RAM didn't make any sense.

Amiga 500 / Amiga 2000

1st generation Amiga (OCS)
MSRP 700$ / 1,500$

Commodore split the Amiga into two classes. The Amiga 500 for the home computer enthusiast (with a price just above the Atari ST) and the Amiga 2000 for professional users with enhanced expandability. Base performance figures for both machines are the same and also barely differ from the Amiga 1000. Memory was extended, bringing it up to specs with the Atari ST models.

Atari 520STE, Atari 1040STE

2nd generation Atari
Available Colors 12bit 4,096 colors
Most Colors 320×200 16 colors
Highest Resolution 640×400 2 colors
Audio 8bit 50kHz 2 channels

Atari finally tried to expand the graphic and sound capabilities of the Atari ST, but fails to match the levels set by the Amiga 1000 four years earlier. But the addition of a hardware blitter (just like inside of the Amiga) meant that the performance gap was closing.

Amiga 3000

2nd generation Amiga (ECS)
MSRP 3,400$

Atari TT

3rd generation Atari
68030 25Mhz CPU 68030 32Mhz
68882 25Mhz FPU 68882 32Mhz
2MB RAM Memory 2MB RAM
320×256 64 colors Most Colors 320×480 256 colors
1280×512 4 colors Highest Resolution 1280×960 2 colors

Commodore released the Amiga 3000 with specs making it a high end graphics workstation (with a suitable price tag to match). The graphics capabilities were also improved with the ECS chipset, but only marginally. Zorro III slots were added delivering lightning fast access for expansion cards to the Amiga hardware.

Atari released the Atari TT (thirty two) which finally exceeds the Amiga with CPU power as well as in the graphics and sound department.

Amiga 1200, Amiga 4000

3rd generation Amiga (AGA)
MSRP 600$ - 3,700$

Atari Falcon

4th generation Atari
68020 14Mhz
68EC030 25Mhz
68040 25Mhz
CPU 68030 16Mhz
2MB RAM Memory 1MB RAM
24bit 16,777,216 colors Available Colors 18bit  262,144 colors
640×512 256 colors Most Colors 640×400 65,536 colors
1440×580 262,144 colors Highest Resolution 640×480 256 colors
Audio 16bit 50kHz 8 channels

The AGA chipset came out, doubling the color deth to 24bit colors and allowing up to 8 bitplanes at once, making it possible to use up to 256 colors at once in many screen modes (not only lowres). But sadly the performance of other components wasn't improved. The blitter now had to cope with much more data for the new screen modes, but couldn't move it around any faster, making it even slower with these now high color screen modes. At the same time Motorola was struggling to keep up with the advances that Intel was making, regarding it's lines of cpus.

The rumoured AAA chipset could have rectified some of this but Commodore itself was beginning to struggle.
With a lack of funding only small

The Atari Falcon, just like the Amiga, is a mixed bag. Nice features that the Amiga was still missing, like the chunky screen modes, a DSP and true color screen modes, are hampered by slow memory and an insufficient bus system.
Atari itself soon stops further development and tries to focus on the Jaguar handheld console.

Looking at these numbers I must say that the first Amiga was superior to the Atari ST. The Amiga was technically the better computer, but also more expensive and the custom hardware was more difficult to develop for.

Developers struggled at first to utilize the custom processors properly. Later Atari suffered the same fate after adding custom processors itself. Making matters worse was that every change in hardware split the market even further making it even more difficult to develop for new hardware if the adoption rate was not high enough.

In the end both Commodore and Atari lost the race.

On a side note: I find it very poor that Commodore never even once improved the sound capabilities of the Amiga. In 1985 the Amiga's sound chip was revolutionary, but by 1992 all other systems had surpassed it.