" When I try and println an array of ~41,000 place objects my program crashes"
Well, don't println it, then. I don't see the point to get so many lines in the PDE console anyway.

Okay. I printed it to a file and it didn't crash which it good but still don't get the string places[j]. I get

ScatterPlotData$Place@1ba6076
ScatterPlotData$Place@112e7f7
ScatterPlotData$Place@3b1f38
ScatterPlotData$Place@17ec9f7
ScatterPlotData$Place@fd918a
ScatterPlotData$Place@15e2075
ScatterPlotData$Place@a522a6
ScatterPlotData$Place@1860038
ScatterPlotData$Place@787c16
ScatterPlotData$Place@1a9d1b
ScatterPlotData$Place@140984b
etc.

I should get a string with place(zip, name, x, y) right?

Thank you.

Yes, what you see is the default print out of a Java class: its class name (here Place is an inner class of your sketch's class, ScatterPlotData) followed by its id in the JVM.
Simple, very useful trick: overload the default toString() method of a class to get useful debugging information.
For example, instead of your draw() method, which currently doesn't do what it promises (ie. no display on screen, but output on console), you can define toString() with almost the same code:

1.   String toString() { // Must return a String
   
2.     float xx = TX(x);
3.     float yy = TY(y);
4.     return xx + "  " + yy + "  " + name;
5.   }

Of course, you can change the returned value to follow another format (using tabs, commas, or whatever separator, changing order of variables, etc.).

That is a very helpful tool thank you.

I think I am able to see the problem now. Which is when I ask it to file.println (line 45). I am getting only two columns of values instead of zip, name, x, and y.

Shouldn't places[j] return a string with zip, name, x, y instead of:
466.41153  66.615585
466.41153  66.615585
515.0676  20.656845
512.8938  20.821766
512.95935  20.975374

With this code I expect to see printed in the console the same that is printed in the file when I loop through the array of places. But in the console I see the zip, name, x, y and in the file I just see that double column above.

1. String[] data;
2. Place[] places;
3. int totalCount, zip;
4. int placeCount = 0;
5. float Xmin, Xmax, Ymin, Ymax, x, y;
6. float mapX1, mapX2, mapY1, mapY2;
7. String name;
8. color backgroundColor = color(152, 151, 141);
9. color highlightedColor = color(247, 237, 25);
10. color unhighlightedColor = backgroundColor;
11. PrintWriter file;
12. void setup() {
13.   size(720, 453, P3D);
14.  
15.   mapX1 = 30.0;
16.   mapX2 = width - mapX1;
17.   mapY1 = 20.0;
18.   mapY2 = height - mapY1;
19.  
20.   readData(data);    //output is Place(zip name x y)
21. }
22. public void draw() {
23.   background(backgroundColor);
24.   for(int i=0; i<placeCount; i++) {
25.     places[i].toString();
26.   }
27. }
28. float TX(float x) {
29.   return map(x, Xmin, Xmax, mapX1, mapX2);
30. }
31. float TY(float y) {
32.   return map(y, Ymin, Ymax, mapY1, mapY2);
33. }
34. void readData(String[] data) {
35.   file = createWriter("data/file.txt");
36.   data = loadStrings("data/clean.tsv");
37.   parseInfo(data[0]);
38.  
39.   places = new Place[totalCount];
40.   for(int i=1; i<data.length; i++) {    
41.     places[placeCount] = parsePlace(data[i]);
42.     placeCount++;
43.   }
44.   for(int j=0; j<51; j++) {
45.     file.println(places[j].toString());  
46.   }
47.   file.flush();
48.   file.close();
49. }
50. //read header line
51. void parseInfo(String head) {
52.   String[] pieces = split(head, TAB);
53.   totalCount = int(pieces[0]);
54.   Xmin = float(pieces[1]);
55.   Xmax = float(pieces[2]);
56.   Ymin = float(pieces[3]);
57.   Ymax = float(pieces[4]);
58. }
59. Place parsePlace(String pLine) {
60.   String[] pieces = split(pLine, TAB);
61.   zip = int(pieces[0]);
62.   x = float(pieces[1]);
63.   y = float(pieces[2]);
64.   name = pieces[3] + ", " + pieces[4];
65.   println(zip +"  "+ name +"  "+ x +"  "+ y);
66.   return new Place(zip, name, x, y);
67. }
68. class Place {
69.   String name;
70.   int zip;
71.   float x;
72.   float y;
73.  
74.   Place(int zip, String name, float x, float y) {
75.     this.name = name;
76.     this.zip = zip;
77.     this.x = x;
78.     this.y = y;
79.   }
80.  
81.   String toString() {
82.     float xx = TX(x);
83.     float yy = TY(y);
84.     return xx + "  " + yy;
85.   }
86. }

Thank you again.

The loop in draw() isn't useful as toString() doesn't do anything visible and you discard (ignore) the return value.
Perhaps you wanted to keep a draw() method in your class.

I forgot to tell that toString() is a method that every object in the JVM has, so methods like println automatically invoke it (they take Object as parameter): no need to call it explicitly.
So instead of file.println(places[j].toString()); you can write file.println(places[j]);

You get different results because you have not adjusted toString to the output you want.
Instead of return xx + "  " + yy;
use return zip + "  " + name + "  " + x + "  " + y;
or return zip + "  " + name + "  " + xx + "  " + yy; depending on the result you really want.